Contacts of the helix formed by residues 48 - 69 (chain 2) 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 GLU 48 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422 ARG* 4.2 18.1 - - + +
442 ASN* 3.1 15.3 + - + +
452 VAL* 5.3 4.7 - - - +
472 ALA* 1.3 74.8 - - - +
492 LEU* 1.3 58.4 + - - +
502 VAL 3.1 5.0 + - - -
512 HIS* 2.8 36.4 + - + -
522 SER* 3.6 4.7 + - - -
3052 CLA 3.7 31.2 - - + +
3062 CLA 4.2 37.2 - - + +
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Residues in contact with LEU 49 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452 VAL 3.6 12.1 - - - +
462 GLN* 3.1 42.8 - - + +
472 ALA 2.9 1.0 - - - -
482 GLU* 1.3 78.1 - - - +
502 VAL* 1.3 71.2 + - + +
522 SER* 3.3 20.1 + - - -
532 ARG* 3.7 7.3 + - - +
1662 ASN* 6.1 0.2 - - - +
3052 CLA 3.2 29.6 - - + +
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Residues in contact with VAL 50 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462 GLN 4.9 3.1 - - - +
472 ALA* 2.8 11.8 + - - +
492 LEU* 1.3 102.7 - - + +
512 HIS* 1.3 50.1 + - - +
522 SER 3.2 3.6 - - - +
532 ARG* 4.5 20.1 - - + +
542 TRP* 2.4 43.8 + - + +
1092 ARG* 5.2 9.9 - - - +
1102 TRP* 4.8 13.0 - - + +
1132 ILE* 5.6 2.9 - - + -
3102 CLA 3.7 10.7 - - - +
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Residues in contact with HIS 51 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472 ALA 3.8 3.4 + - - +
482 GLU* 2.8 35.8 + - + -
502 VAL* 1.3 74.0 - - - +
522 SER* 1.3 58.7 + - - +
542 TRP* 2.9 4.6 - - - +
552 ALA* 2.4 35.4 + - + +
562 MET* 5.3 3.2 - - + +
3052 CLA 5.6 4.5 - - + -
3062 CLA 3.6 68.2 + + + +
3102 CLA 2.6 53.1 - + + +
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Residues in contact with SER 52 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482 GLU 3.6 5.6 + - - -
492 LEU* 3.3 24.3 + - - -
512 HIS* 1.3 79.7 - - - +
532 ARG* 1.3 56.2 + - - +
542 TRP 2.8 4.2 + - - -
552 ALA 2.9 0.9 + - - -
562 MET* 2.7 48.1 + - - +
1662 ASN* 4.0 3.5 + - - -
1692 LEU* 2.9 39.9 - - - +
3052 CLA 4.8 4.0 - - - -
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Residues in contact with ARG 53 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492 LEU 3.7 9.7 + - - +
502 VAL* 4.8 19.5 - - + +
522 SER* 1.3 77.8 + - - +
542 TRP* 1.3 58.0 + - - +
562 MET* 4.2 1.6 - - - +
572 LEU* 3.3 46.6 - - + +
1092 ARG* 2.9 36.0 - - - +
1612 THR* 5.8 4.0 + - - +
1652 LYS* 5.6 10.1 - - + -
3022 CLA 3.9 35.9 - - - +
3092 CLA 5.1 4.9 - - - -
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Residues in contact with TRP 54 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502 VAL* 2.4 34.3 + - + +
512 HIS 2.9 4.1 - - - +
522 SER 2.8 0.8 - - - -
532 ARG* 1.3 79.7 - - - +
552 ALA* 1.3 68.4 + - - +
562 MET 3.0 1.5 + - - -
572 LEU* 4.6 2.4 - - - +
582 GLY* 3.5 12.8 + - - -
1062 GLU* 3.2 54.1 - - + -
1092 ARG* 2.6 63.5 - - + +
1102 TRP* 4.8 1.8 - - - -
3092 CLA 4.9 17.5 - + + -
3102 CLA 2.4 60.0 + + + +
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Residues in contact with ALA 55 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512 HIS* 2.4 26.9 + - + +
522 SER 2.9 0.6 + - - -
542 TRP* 1.3 74.8 - - - +
562 MET* 1.3 90.6 + - + +
582 GLY* 3.5 2.3 - - - -
592 ALA* 3.2 19.6 + - - +
3062 CLA 5.9 6.7 - - + -
3102 CLA 3.6 21.1 - - + -
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Residues in contact with MET 56 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512 HIS* 5.3 3.8 - - + +
522 SER* 2.7 40.7 + - - +
542 TRP 3.0 2.2 + - - -
552 ALA* 1.3 105.6 - - + +
572 LEU* 1.3 68.0 + - - +
582 GLY 2.8 0.4 - - - -
592 ALA* 2.8 12.2 + - + +
602 ALA 3.4 0.9 + - - -
1682 ARG* 3.2 32.4 - - + +
1692 LEU* 3.3 43.3 - - + +
1722 LEU* 3.1 28.3 - - + +
1732 ALA 5.6 0.4 - - - -
3052 CLA 4.4 2.5 - - - -
3062 CLA 6.5 1.1 - - + -
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Residues in contact with LEU 57 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522 SER 4.4 0.8 + - - -
532 ARG* 3.3 41.0 + - + +
542 TRP* 4.6 2.7 - - - +
562 MET* 1.3 70.8 - - - +
582 GLY* 1.3 73.3 - - - +
602 ALA* 2.6 41.0 + - - +
1652 LYS* 4.7 19.5 - - + +
1682 ARG* 3.7 17.0 - - - +
3092 CLA 3.3 81.7 - - + +
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Residues in contact with GLY 58 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542 TRP 3.5 8.5 + - - -
552 ALA 3.5 8.1 - - - -
562 MET 2.8 1.6 - - - -
572 LEU* 1.3 88.0 - - - +
592 ALA* 1.3 54.8 + - - -
602 ALA 2.9 5.2 - - - -
612 GLY* 2.9 23.9 + - - -
622 ILE 4.1 0.7 + - - -
3092 CLA 4.7 12.4 - - - -
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Residues in contact with ALA 59 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552 ALA 3.2 10.8 + - - +
562 MET* 2.8 9.1 + - + +
582 GLY* 1.3 68.1 - - - -
602 ALA* 1.3 54.1 + - - +
622 ILE* 3.2 16.8 + - + +
632 PHE* 2.8 38.0 + - - +
1722 LEU* 3.2 38.4 - - + -
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Residues in contact with ALA 60 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562 MET 3.4 3.0 + - - +
572 LEU* 2.6 22.3 + - - +
592 ALA* 1.3 73.6 - - - +
612 GLY* 1.3 55.6 + - - +
632 PHE* 2.8 51.8 + - + -
642 ILE* 3.2 15.8 + - + +
652 PRO* 3.4 3.2 - - - +
1682 ARG* 4.9 1.3 - - - -
3092 CLA 5.1 12.8 - - + -
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Residues in contact with GLY 61 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582 GLY 2.9 12.8 + - - -
602 ALA* 1.3 76.9 - - - +
622 ILE* 1.3 58.9 + - - +
652 PRO* 2.7 29.8 - - - +
3092 CLA 5.1 11.9 - - - +
3152 CLA 4.1 19.6 - - - +
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Residues in contact with ILE 62 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582 GLY 4.1 1.4 + - - -
592 ALA* 3.2 23.9 + - + +
602 ALA 2.9 2.0 + - - -
612 GLY* 1.3 79.4 - - - +
632 PHE* 1.3 70.2 + - + +
642 ILE 3.5 0.4 - - - -
662 GLU* 2.8 60.0 + - + +
1722 LEU* 5.2 2.2 - - + -
3152 CLA 4.8 23.1 - - + -
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Residues in contact with PHE 63 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592 ALA 2.8 11.2 + - - +
602 ALA* 2.8 41.2 + - + -
622 ILE* 1.3 77.9 - - + +
642 ILE* 1.3 89.0 + - + +
662 GLU* 4.4 2.5 - - - -
672 PHE* 3.4 33.5 + - + -
1642 ILE* 6.0 3.4 - - + -
1682 ARG* 3.2 37.0 - - - -
1712 MET* 4.6 9.6 - - + -
1722 LEU* 3.5 23.3 - - + -
1752 MET* 6.5 0.2 - - + -
3032 CLA 3.5 46.7 - + + +
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Residues in contact with ILE 64 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602 ALA* 3.2 7.4 + - + +
632 PHE* 1.3 93.6 - - + +
652 PRO* 1.4 71.8 - - + +
672 PHE* 5.4 1.3 - - + -
682 LEU* 2.6 68.5 + - + +
3032 CLA 3.3 46.7 - - + -
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Residues in contact with PRO 65 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602 ALA 3.4 3.6 - - - +
612 GLY* 2.7 33.9 - - - +
622 ILE* 3.6 2.2 - - + +
642 ILE* 1.4 99.5 - - + +
662 GLU* 1.3 70.1 + - - +
682 LEU* 3.4 15.1 - - + +
692 THR* 2.8 15.6 + - - +
3152 CLA 4.6 32.5 - - + +
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Residues in contact with GLU 66 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622 ILE* 2.8 51.3 + - + +
632 PHE* 3.8 7.0 - - - +
652 PRO* 1.3 73.5 - - - +
672 PHE* 1.3 80.1 + - + +
692 THR* 2.1 51.2 + - + -
1822 ILE* 4.7 12.1 - - - +
3152 CLA 5.9 2.1 - - - +
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Residues in contact with PHE 67 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632 PHE* 3.4 26.4 + - + -
642 ILE* 6.2 0.9 - - + -
662 GLU* 1.3 101.0 - - + +
682 LEU* 1.3 69.7 + - - +
692 THR* 3.1 8.3 + - - -
712 LEU 5.3 0.9 + - - -
1752 MET* 5.4 21.8 - - + -
1782 TRP* 6.4 0.7 - + + -
1822 ILE* 4.7 19.1 - - + -
2052 PHE* 5.5 17.0 - + - -
2062 ALA 6.4 2.0 - - - -
2072 ALA* 6.4 2.2 - - + -
3032 CLA 6.5 0.4 - - + -
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Residues in contact with LEU 68 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642 ILE* 2.6 48.7 + - + +
652 PRO* 3.4 15.7 - - + +
662 GLU 2.9 1.4 + - - -
672 PHE* 1.3 76.2 - - - +
692 THR* 1.3 61.9 + - - +
702 LYS* 2.4 38.5 + - + +
712 LEU 4.0 1.4 + - - -
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Residues in contact with THR 69 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652 PRO 2.8 11.9 + - - +
662 GLU* 2.1 38.0 + - + +
672 PHE* 3.1 9.0 + - - -
682 LEU* 1.3 70.5 + - - +
702 LYS* 1.3 94.1 + - - +
712 LEU* 4.3 5.0 + - - -
3152 CLA 6.6 0.7 - - + -
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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