Contacts of the helix formed by residues 37 - 60 (chain 4) in PDB entry 2WSF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 37 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354 GLU 3.2 11.4 - - - +
364 ASN* 1.4 82.1 + - - +
384 ARG* 1.3 67.7 + - + +
394 TRP* 2.4 38.5 - - - +
414 VAL* 3.5 9.2 + - - +
1314 VAL* 4.0 35.9 - - + +
1344 PRO* 6.4 0.9 - - + -
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Residues in contact with ARG 38 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364 ASN* 2.5 38.8 + - - +
374 LEU* 1.3 80.9 - - + +
394 TRP* 1.3 90.0 + - - +
404 PHE* 4.3 13.7 - - - -
414 VAL* 4.2 0.5 - - - +
424 GLN* 3.1 24.6 + - - +
1094 ILE* 4.8 23.3 - - + +
1104 LYS* 6.2 0.7 - - - +
1204 ILE* 5.2 14.8 - - + -
1314 VAL* 5.0 4.9 + - - +
146F ASN* 5.9 2.6 + - - +
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Residues in contact with TRP 39 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344 PRO* 5.9 1.1 - - + -
354 GLU* 5.3 4.5 - - - -
364 ASN* 2.0 88.2 + - + +
374 LEU 2.4 43.7 - - - -
384 ARG* 1.3 98.1 - - - +
404 PHE* 1.3 108.3 + + + +
414 VAL* 3.0 25.6 - - + +
424 GLN* 3.5 2.4 + - - +
434 ALA 3.3 8.7 + - - -
143F GLU* 5.9 2.9 - - - -
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Residues in contact with PHE 40 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364 ASN 5.0 0.2 - - - -
384 ARG* 4.3 15.5 - - - -
394 TRP* 1.3 149.1 - + + +
414 VAL* 1.3 58.8 + - - -
434 ALA* 2.5 45.7 - - + +
444 GLU* 3.4 8.7 + - - +
3134 CLA 4.8 29.4 - + + -
138F VAL* 6.2 5.2 - - + -
142F ARG* 4.9 19.7 - - + -
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Residues in contact with VAL 41 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374 LEU 3.6 9.0 - - - +
384 ARG 4.2 0.4 - - - +
394 TRP* 3.0 22.5 - - + +
404 PHE* 1.3 75.0 - - - +
424 GLN* 1.3 70.4 + - - +
444 GLU* 3.2 18.8 + - - +
454 LEU* 3.6 13.0 + - + +
1194 PRO 5.7 1.6 - - - +
1204 ILE 6.4 0.7 - - - -
1214 PHE* 6.3 2.0 - - - -
1224 LYS* 5.5 6.5 - - - +
1414 LEU* 4.5 24.7 - - + -
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Residues in contact with GLN 42 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384 ARG 3.1 18.9 + - - +
394 TRP 3.8 2.2 - - - +
414 VAL* 1.3 78.7 - - - +
434 ALA* 1.3 69.5 + - - +
444 GLU 2.9 1.4 + - - -
454 LEU* 3.7 10.7 + - + +
464 VAL* 3.2 23.8 - - + +
1054 ARG* 4.2 25.6 - - - +
1094 ILE* 4.2 17.1 - - + +
1194 PRO* 2.8 30.1 - - - +
1204 ILE* 2.8 53.2 - - - +
3124 CLA 4.6 0.4 - - - -
3134 CLA 4.8 2.7 - - + -
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Residues in contact with ALA 43 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394 TRP 3.3 5.3 + - - -
404 PHE* 2.5 57.6 - - + +
424 GLN* 1.3 77.5 - - - +
444 GLU* 1.3 58.2 - - - +
474 ASN* 2.8 17.7 - - - +
3134 CLA 3.0 27.3 - - + +
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Residues in contact with GLU 44 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404 PHE 3.4 7.3 + - - +
414 VAL* 3.2 11.6 + - - +
424 GLN 2.9 2.6 + - - -
434 ALA* 1.3 74.2 - - - +
454 LEU* 1.3 54.6 + - - +
464 VAL 2.4 4.3 + - - -
474 ASN* 2.2 46.4 + - - -
484 GLY* 3.1 3.8 + - - +
1614 LEU* 4.9 16.3 - - + +
3084 CLA 3.9 54.4 + - + +
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Residues in contact with LEU 45 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414 VAL* 3.6 9.8 + - + +
424 GLN* 3.7 23.3 + - - +
444 GLU* 1.3 77.7 - - - +
464 VAL* 1.3 58.9 + - + +
484 GLY* 3.7 5.4 - - - +
494 ARG* 2.7 70.5 + - + +
1184 ASP 5.2 0.2 - - - +
1194 PRO* 3.3 48.0 - - + +
1224 LYS* 5.4 8.5 - - - -
3054 CLA 5.5 3.4 - - + -
3124 CLA 4.7 13.0 - - + -
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Residues in contact with VAL 46 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424 GLN* 3.2 22.0 - - + +
444 GLU 2.4 9.7 + - - -
454 LEU* 1.3 75.2 - - + +
474 ASN* 1.3 59.4 + - - -
494 ARG* 5.2 1.8 - - - -
504 TRP* 3.3 44.2 + - + +
1054 ARG* 3.2 36.8 - - - +
3124 CLA 5.5 17.0 - - + -
3134 CLA 3.2 34.6 - - + +
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Residues in contact with ASN 47 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434 ALA* 2.8 24.8 - - - +
444 GLU* 2.2 25.4 + - + +
464 VAL* 1.3 66.4 - - - +
484 GLY* 1.3 58.5 + - - +
504 TRP* 3.1 2.6 + - - +
514 ALA* 2.7 36.2 + - - +
1614 LEU* 3.1 24.6 - - + +
3134 CLA 3.8 18.5 - - - +
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Residues in contact with GLY 48 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444 GLU* 3.1 8.6 + - - -
454 LEU* 3.6 6.7 - - - -
474 ASN* 1.3 79.9 - - - +
494 ARG* 1.3 56.5 + - - +
514 ALA* 3.6 2.6 - - - +
524 MET* 2.9 36.4 + - - +
1574 GLY* 3.3 28.1 - - - +
1614 LEU* 3.4 6.9 - - - +
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Residues in contact with ARG 49 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454 LEU* 2.7 49.7 + - + +
464 VAL* 5.1 1.8 - - - +
484 GLY* 1.3 71.0 - - - -
504 TRP* 1.3 56.8 + - - +
524 MET* 3.5 22.4 - - + +
534 LEU* 2.8 38.1 + - + +
1184 ASP 5.1 2.2 + - - -
1224 LYS* 6.2 1.2 - - - +
1504 LYS* 5.1 13.5 - - - +
1534 GLU* 3.1 44.5 + - - +
3054 CLA 3.4 69.5 - - + +
3124 CLA 5.4 12.6 - - + -
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Residues in contact with TRP 50 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464 VAL* 3.3 38.3 + - + +
474 ASN* 3.1 3.0 + - - +
494 ARG* 1.3 75.0 - - - +
514 ALA* 1.3 55.0 + - - +
524 MET 3.3 1.1 - - - -
534 LEU* 3.8 30.9 - - + +
544 GLY* 2.8 30.1 + - - -
1024 GLU* 5.9 6.3 - - + -
1054 ARG* 6.0 1.6 - - - -
3104 CLA 5.4 8.1 - - + +
3124 CLA 4.4 33.2 - + + -
3134 CLA 3.8 59.2 - + + -
3144 CLA 6.1 7.4 - + + -
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Residues in contact with ALA 51 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474 ASN 2.7 21.6 + - - +
484 GLY 3.6 2.7 - - - +
504 TRP* 1.3 70.1 - - - +
524 MET* 1.3 65.4 + - - +
544 GLY* 3.5 1.8 + - - +
554 VAL* 3.2 31.0 + - - +
1604 MET* 3.6 6.3 - - - +
1614 LEU* 3.4 38.6 - - + +
1644 LEU* 5.3 8.3 - - + -
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Residues in contact with MET 52 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484 GLY 2.9 25.1 + - - +
494 ARG* 3.5 22.0 - - + +
514 ALA* 1.3 77.5 - - - +
534 LEU* 1.3 66.0 + - + +
554 VAL* 3.3 12.8 + - - +
564 ALA* 3.4 8.0 + - - +
1534 GLU* 3.9 27.4 - - - +
1564 ASN* 3.1 48.7 - - + +
1574 GLY* 3.7 9.2 - - - +
1604 MET* 3.2 25.5 - - + +
3054 CLA 5.9 4.5 - - + -
3064 CLA 6.3 1.6 - - + -
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Residues in contact with LEU 53 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494 ARG* 2.8 32.0 + - + +
504 TRP* 3.8 27.6 - - + +
514 ALA 3.4 0.2 - - - -
524 MET* 1.3 76.2 - - + +
544 GLY* 1.3 58.7 + - - +
564 ALA* 2.5 38.6 + - + +
574 GLY 3.3 2.1 + - - -
3054 CLA 4.5 24.5 - - + -
3104 CLA 4.2 50.0 - - + +
3124 CLA 5.8 9.4 - - + -
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Residues in contact with GLY 54 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504 TRP* 2.8 22.4 + - - -
514 ALA* 3.8 3.1 - - - -
524 MET 3.5 0.4 - - - -
534 LEU* 1.3 70.3 - - - +
554 VAL* 1.3 58.5 + - - +
574 GLY* 2.9 22.7 + - - -
584 MET 3.8 1.7 + - - -
1644 LEU* 5.8 8.1 - - - -
3104 CLA 5.3 11.9 - - - +
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Residues in contact with VAL 55 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514 ALA 3.2 15.8 + - - +
524 MET 3.3 12.5 + - - +
534 LEU 2.7 5.1 + - - -
544 GLY* 1.3 71.2 - - - +
564 ALA* 1.3 58.6 + - - +
574 GLY 3.0 0.9 - - - -
584 MET* 3.1 16.0 + - + +
594 LEU* 2.8 26.3 + - - +
1604 MET* 3.8 38.4 - - + +
1634 PHE* 4.6 9.4 - - + -
1644 LEU* 4.8 8.7 - - + +
1674 ILE* 3.9 27.8 - - + -
3064 CLA 5.2 6.7 - - + -
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Residues in contact with ALA 56 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524 MET 3.4 6.2 + - - +
534 LEU* 2.5 23.1 + - + +
554 VAL* 1.3 68.2 - - - +
574 GLY* 1.3 65.6 + - - +
584 MET 3.7 0.2 - - - -
594 LEU* 3.2 24.7 + - + +
604 LEU* 4.0 3.8 + - - +
3104 CLA 4.1 40.0 + - + +
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Residues in contact with GLY 57 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534 LEU 3.3 2.6 + - - -
544 GLY* 2.9 16.7 + - - -
564 ALA* 1.3 76.1 - - - +
584 MET* 1.3 53.1 + - - -
604 LEU* 2.7 37.1 - - - +
3104 CLA 4.9 28.1 + - - -
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Residues in contact with MET 58 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544 GLY 3.8 3.0 + - - -
554 VAL* 3.1 18.4 + - + +
574 GLY* 1.3 72.9 - - - +
594 LEU* 1.3 90.8 + - + +
604 LEU 2.4 19.8 + - - -
614 PRO* 2.4 27.9 - - + +
624 GLU* 2.9 40.4 - - - +
1634 PHE* 6.2 5.8 - - + -
1674 ILE* 4.6 27.8 - - + -
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Residues in contact with LEU 59 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554 VAL 2.8 17.5 + - - +
564 ALA* 3.2 20.8 + - - +
584 MET* 1.3 96.0 - - + +
604 LEU* 1.3 70.8 + - - +
614 PRO* 3.3 1.0 - - - +
624 GLU* 3.8 8.9 + - - +
634 VAL* 5.8 1.2 - - - +
3064 CLA 6.2 3.8 - - + -
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Residues in contact with LEU 60 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564 ALA 4.0 3.1 + - - +
574 GLY 2.7 30.3 - - - +
584 MET 2.4 8.4 + - - +
594 LEU* 1.3 79.0 - - - +
614 PRO* 1.4 63.9 - - + +
624 GLU* 2.6 15.8 + - - -
634 VAL* 4.0 7.4 + - - +
644 PHE* 4.2 10.5 - - - +
674 ILE* 3.6 28.5 - - + +
684 GLY* 5.6 0.9 - - - -
714 ASN* 6.0 0.7 - - - +
3104 CLA 4.3 59.7 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il