Contacts of the helix formed by residues 32 - 48 (chain 8) in PDB entry 6CP3
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 32 (chain 8).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1587 TRP* 3.5 27.3 - - + -
278 PHE* 3.1 33.4 + - + +
288 SER* 4.4 2.2 - - - +
318 PHE* 1.3 76.7 - - - +
338 PRO* 1.3 63.1 - - + +
358 ILE* 3.0 24.1 + - - +
368 LEU* 3.0 10.0 + - - +
66X TYR* 4.5 11.7 - - + -
86X PHE* 3.6 34.1 - - + +
87X PRO* 4.1 18.8 - - + +
90X PHE* 3.6 37.2 - - + -
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Residues in contact with PRO 33 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497 VAL* 4.6 1.1 - - + +
1537 VAL* 4.2 19.7 - - + -
1587 TRP* 4.4 4.5 - - + -
288 SER 3.3 25.4 - - - +
298 GLN 3.9 6.7 - - - +
308 PHE 3.4 11.0 - - - +
328 LEU* 1.3 88.2 - - + +
348 MET* 1.3 59.1 + - - +
358 ILE 3.1 0.2 - - - -
368 LEU* 3.6 11.1 - - + +
378 ARG* 2.9 33.0 + - - +
3J LYS 5.7 0.4 - - - +
5J PHE* 3.5 34.8 - - + -
7J THR* 4.7 2.7 - - + -
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Residues in contact with MET 34 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308 PHE 3.1 13.0 + - - +
318 PHE* 3.3 32.8 - - - +
338 PRO* 1.3 76.5 - - - +
358 ILE* 1.3 66.5 + - + +
378 ARG* 4.0 12.5 - - - +
388 LEU* 3.7 21.9 + - + +
2J LEU* 3.7 36.8 - - + -
3J LYS 6.1 1.8 - - - +
5J PHE* 5.7 0.4 - - - -
44X TYR* 4.0 27.1 - - + +
45X THR* 5.8 0.2 - - - -
48X ASN* 4.1 23.3 - - + +
51X ASN* 5.3 0.7 - - - +
59X LEU* 5.5 5.8 - - + -
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Residues in contact with ILE 35 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318 PHE 3.4 20.6 - - - +
328 LEU* 3.0 8.1 + - - +
348 MET* 1.3 84.9 - - + +
368 LEU* 1.3 60.9 + - - +
378 ARG 3.2 1.3 - - - -
388 LEU* 2.9 33.2 + - + +
398 TYR* 3.0 31.1 + - + +
44X TYR* 3.8 23.6 - - + -
59X LEU* 5.2 8.5 - - + -
62X GLN* 4.4 17.9 - - + +
63X GLU* 3.6 25.8 - - - +
66X TYR* 4.9 15.5 - - + -
90X PHE* 6.2 2.9 - - + -
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Residues in contact with LEU 36 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497 VAL* 3.8 28.3 - - + +
1527 MET* 3.7 36.1 - - + -
1537 VAL* 4.7 7.2 - - + -
1587 TRP* 3.6 43.1 - - + +
1607 VAL* 4.9 5.4 - - + -
328 LEU 3.0 7.8 + - - +
338 PRO* 3.3 15.0 + - + +
358 ILE* 1.3 77.6 - - - +
378 ARG* 1.3 55.4 + - - +
398 TYR* 3.3 10.8 + - - +
408 VAL* 2.9 41.2 + - + +
66X TYR* 4.1 9.8 + - - +
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Residues in contact with ARG 37 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357 VAL* 3.7 21.2 + - + +
1367 ASP* 3.5 24.8 + - - -
1397 THR* 2.5 37.0 + - - +
1457 ILE* 5.1 9.2 - - + +
1467 ASP* 5.6 3.3 + - - +
1497 VAL* 3.8 29.4 - - + -
338 PRO 2.9 19.1 + - - +
348 MET* 4.0 11.0 - - - +
358 ILE 3.2 0.2 - - - -
368 LEU* 1.3 76.0 - - - +
388 LEU* 1.3 56.8 + - - +
408 VAL* 3.8 0.7 - - - +
418 SER* 2.9 32.4 + - - -
3J LYS* 3.5 37.7 - - - +
5J PHE* 3.6 21.0 - - - -
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Residues in contact with LEU 38 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357 VAL* 3.8 25.4 - - + -
348 MET* 3.7 17.7 - - + +
358 ILE* 2.9 24.4 + - + +
378 ARG* 1.3 78.4 - - + +
398 TYR* 1.3 57.9 + - + +
418 SER* 2.7 17.2 + - - -
428 ARG* 3.0 33.6 + - - +
48X ASN* 6.1 3.6 - - - +
51X ASN* 5.3 1.3 - - - -
52X LYS 3.4 25.4 - - - +
53X ILE* 4.4 7.2 - - - +
55X GLY* 5.6 2.0 - - - -
59X LEU* 3.7 30.1 - - + -
63X GLU* 5.1 5.4 - - - +
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Residues in contact with TYR 39 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1607 VAL* 4.0 26.7 - - + -
1637 TYR* 3.3 46.9 - + + -
358 ILE* 3.0 41.3 + - + -
368 LEU* 3.3 11.2 + - - +
388 LEU* 1.3 77.6 - - + +
408 VAL* 1.3 58.3 + - - +
428 ARG* 3.3 4.5 + - - +
438 LEU* 3.0 31.5 + - - +
63X GLU* 2.8 31.0 + - - -
66X TYR* 3.3 30.5 - + - -
67X ASP* 2.6 30.8 + - - -
70X MET* 5.4 3.8 - - + -
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Residues in contact with VAL 40 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1447 GLU* 5.9 1.8 - - - +
1457 ILE* 4.6 18.6 - - + +
1487 LYS* 4.8 11.7 - - + -
1497 VAL* 3.8 20.9 - - + -
1527 MET* 4.2 19.5 - - + -
1607 VAL* 4.8 7.6 - - + -
368 LEU* 2.9 39.0 + - + +
378 ARG 4.1 1.1 - - - +
398 TYR* 1.3 77.1 - - + +
418 SER* 1.3 57.3 + - - +
438 LEU* 3.5 6.6 + - + +
448 PHE* 2.9 34.7 + - + +
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Residues in contact with SER 41 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357 VAL* 3.9 15.7 - - - +
1387 LEU* 4.0 23.8 - - - -
1457 ILE* 4.8 14.1 - - - +
378 ARG 2.9 17.1 + - - -
388 LEU* 2.7 25.5 + - - -
408 VAL* 1.3 74.7 - - - +
428 ARG* 1.3 60.6 + - - +
448 PHE* 3.3 4.8 + - - +
458 ILE* 2.9 36.9 + - - +
53X ILE* 4.5 3.7 - - - +
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Residues in contact with ARG 42 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1637 TYR* 4.0 19.6 + - + -
1677 PHE* 3.7 29.1 - - + -
1707 LEU* 5.9 0.6 - - - +
388 LEU* 3.0 27.6 + - - +
398 TYR* 3.8 4.2 - - - +
418 SER* 1.3 81.6 + - - +
438 LEU* 1.3 57.7 + - - +
458 ILE* 3.3 8.6 + - - +
468 SER* 2.9 29.1 + - - -
53X ILE* 2.7 42.7 + - + +
54X ILE* 3.0 24.5 + - - +
55X GLY* 3.4 10.5 + - - +
63X GLU* 4.4 17.5 + - - +
84Z ARG* 5.1 3.6 - - - +
88Z VAL* 4.1 26.5 - - + +
92Z LEU* 4.6 5.6 - - + +
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Residues in contact with LEU 43 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1607 VAL* 3.7 18.8 - - + -
1617 PRO 3.3 26.5 - - - +
1627 GLY* 3.6 20.4 - - - +
1637 TYR* 3.8 13.2 - - + -
1667 ARG* 5.3 4.9 - - - +
1677 PHE* 4.8 2.4 - - - -
398 TYR 3.0 17.2 + - - +
408 VAL* 4.1 6.3 - - + +
428 ARG* 1.3 76.5 - - - +
448 PHE* 1.3 60.3 + - + +
468 SER* 4.0 4.9 - - - +
478 LYS* 2.9 55.2 + - + +
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Residues in contact with PHE 44 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1387 LEU* 6.5 1.1 - - + -
1427 LYS* 4.0 37.2 - - + -
1447 GLU* 3.2 35.2 - - + -
1457 ILE* 3.7 20.6 - - + -
408 VAL* 2.9 21.9 + - + +
418 SER 3.8 3.4 - - - +
438 LEU* 1.3 78.4 - - + +
458 ILE* 1.3 64.7 + - + +
478 LYS* 4.8 2.9 - - + -
488 LEU* 3.1 41.1 + - + +
25U ALA* 6.3 2.2 - - + -
29U HIS* 5.6 7.0 - + + -
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Residues in contact with ILE 45 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1387 LEU* 3.8 26.5 - - + -
418 SER 2.9 22.1 + - - +
428 ARG 3.7 4.0 - - - +
448 PHE* 1.3 81.2 - - + +
468 SER* 1.3 64.6 + - - +
488 LEU* 3.3 18.3 + - - +
29U HIS* 4.4 21.3 - - + +
53X ILE* 3.8 15.3 - - + -
92Z LEU* 3.7 25.6 - - + -
95Z SER* 4.1 6.7 + - - +
96Z ARG* 3.8 44.0 - - + +
99Z HIS* 4.9 6.3 + - + -
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Residues in contact with SER 46 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1667 ARG* 2.5 38.6 + - - +
1677 PHE* 4.7 14.4 - - - -
428 ARG 2.9 17.7 + - - -
438 LEU* 4.0 4.3 - - - -
458 ILE* 1.3 79.9 - - - +
478 LYS* 1.3 60.7 + - - +
488 LEU* 4.8 0.9 - - - +
91Z VAL* 5.1 4.0 - - - +
92Z LEU* 5.2 2.0 - - - +
95Z SER* 3.9 27.7 - - - -
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Residues in contact with LYS 47 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1617 PRO 5.7 0.2 - - - -
1627 GLY* 4.2 19.9 + - - -
1657 ASP* 5.0 2.4 + - - -
1667 ARG* 3.1 35.7 - - - +
438 LEU* 2.9 39.8 + - + +
448 PHE* 4.7 3.6 - - + +
468 SER* 1.3 75.9 - - - +
488 LEU* 1.3 72.7 + - - +
22U LYS* 4.1 9.0 + - - -
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Residues in contact with LEU 48 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448 PHE* 3.1 39.2 + - + +
458 ILE* 3.3 9.8 + - - +
468 SER 3.3 3.3 - - - +
478 LYS* 1.3 85.3 - - - +
22U LYS* 3.9 35.1 + - + +
25U ALA* 4.4 18.8 - - + +
26U ASN* 3.6 32.3 - - + +
29U HIS* 4.3 22.9 - - + +
99Z HIS* 3.5 45.3 - - + +
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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) + - + + + + + -
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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