Contacts of the helix formed by residues 28 - 37 (chain A) in PDB entry 6QPA
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 VAL 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A THR* 2.8 25.6 + - - +
27A LYS* 1.3 100.6 - - + +
29A GLY* 1.3 66.3 + - - +
30A PRO 3.5 0.9 - - - -
31A LYS* 3.0 17.4 + - - +
32A VAL* 3.2 12.2 + - + +
102A LEU* 3.5 41.5 - - + +
105A GLY* 5.5 3.8 - - - -
106A CYS* 3.5 22.7 - - - +
224B LEU* 4.6 11.7 - - + -
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Residues in contact with GLY 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR 3.8 1.4 + - - -
25A MET* 3.3 15.6 + - - +
28A VAL* 1.3 76.3 - - - +
30A PRO* 1.3 69.5 - - - +
32A VAL* 3.0 20.1 + - - +
33A CSS 3.2 16.4 + - - -
47A GLN* 4.6 12.1 - - - -
78A GLN* 5.1 6.1 + - - -
106A CYS* 5.5 2.1 - - - -
303A MET* 5.2 2.0 - - - -
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Residues in contact with PRO 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A MET 3.6 6.5 - - - +
26A MET 3.2 26.7 - - - +
27A LYS 4.3 2.0 - - - +
28A VAL 3.8 2.0 - - - +
29A GLY* 1.3 89.0 - - - +
31A LYS* 1.3 58.1 + - + +
33A CSS 3.1 9.2 + - + +
34A ILE* 2.8 43.5 + - + +
303A MET* 4.0 24.7 - - + -
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS* 3.5 32.7 + - - +
28A VAL* 3.0 10.3 + - - +
30A PRO* 1.3 77.0 - - + +
32A VAL* 1.3 61.2 + - - +
34A ILE* 3.4 5.3 + - + +
35A THR* 3.0 27.7 + - - -
102A LEU* 3.6 19.2 - - + +
220B ALA 5.4 0.2 - - - -
221B VAL* 3.1 34.9 + - - +
222B SER* 4.2 2.6 - - - -
223B THR 3.4 24.9 - - - +
224B LEU* 3.8 20.0 - - + +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 3.2 15.9 + - + +
29A GLY* 3.0 9.6 + - - +
31A LYS* 1.3 77.3 - - - +
33A CSS 1.3 58.5 + - - +
35A THR* 3.2 5.1 + - - -
36A THR* 2.7 42.8 + - - +
78A GLN* 5.4 11.7 - - - +
99A ILE* 5.4 11.6 - - + +
102A LEU* 3.9 28.5 - - + -
103A CSS 4.1 26.9 - - - -
106A CYS* 5.5 0.4 - - - -
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Residues in contact with CSS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLY 3.2 13.2 + - - -
30A PRO* 3.1 10.8 + - + +
32A VAL* 1.3 81.2 + - - +
34A ILE* 1.3 67.7 + - + +
36A THR* 3.2 15.0 + - - -
37A ALA* 2.9 26.9 + - - +
42A PHE* 4.9 2.9 - - + -
45A PHE* 3.8 61.2 - - + -
47A GLN* 6.4 0.2 - - - -
78A GLN* 5.5 15.3 - - - -
80A THR* 4.3 13.7 - - - -
303A MET* 6.2 1.6 - - - -
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Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PRO* 2.8 30.9 + - + +
31A LYS* 3.7 6.7 - - + +
32A VAL 3.2 0.2 - - - -
33A CSS 1.3 78.7 + - + +
35A THR* 1.3 64.3 + - - +
37A ALA* 3.4 11.4 + - - +
38A SER* 3.6 9.2 + - - -
218B MET* 3.9 26.7 - - + +
221B VAL* 3.8 30.5 - - + +
222B SER* 3.4 17.9 + - - +
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Residues in contact with THR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LYS 3.0 15.2 + - - -
32A VAL* 3.4 11.0 - - - -
34A ILE* 1.3 76.7 - - - +
36A THR* 1.3 59.3 + - - +
38A SER* 2.9 29.8 + - - -
91A MET* 4.3 0.6 - - - +
95A ASN* 3.5 38.3 - - + +
98A GLU* 4.3 7.6 - - + +
99A ILE* 3.8 20.2 - - + -
102A LEU* 3.7 8.9 - - - +
222B SER* 3.3 23.5 + - - -
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Residues in contact with THR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL* 2.7 31.0 + - - +
33A CSS 3.2 13.6 + - - -
35A THR* 1.3 77.2 - - - +
37A ALA* 1.3 57.3 + - - +
38A SER 3.1 5.7 + - - -
39A HIS* 3.2 10.4 + - - +
42A PHE* 3.4 40.8 - - + +
80A THR* 4.4 8.8 - - + +
82A TRP* 3.5 21.3 - - + -
91A MET* 3.7 24.9 - - + +
99A ILE* 5.7 1.0 - - - +
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A CSS 2.9 16.6 + - - +
34A ILE* 3.4 6.9 + - - +
35A THR 3.3 0.2 - - - -
36A THR* 1.3 73.4 - - - +
38A SER* 1.3 61.0 + - - +
39A HIS 3.1 4.9 + - - +
42A PHE* 3.5 28.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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