Contacts of the helix formed by residues 22 - 36 (chain A) in PDB entry 6CUS
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 SER 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A SER 3.9 1.8 + - - -
21A PRO* 1.3 75.3 - - - +
23A LYS* 1.3 65.4 + - - +
24A LYS* 3.1 9.9 - - - -
25A GLU* 2.7 40.9 + - - +
26A ILE* 3.1 13.0 + - - +
101A IHP 4.4 12.6 - - - -
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Residues in contact with LYS 23 (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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5A ILE* 3.5 31.2 - - + -
9A SER* 4.5 9.6 + - - +
21A PRO 3.9 1.2 + - - -
22A SER* 1.3 73.1 - - - +
24A LYS* 1.3 64.3 + - - +
26A ILE* 3.3 10.6 + - - +
27A GLY* 2.8 28.2 + - - -
101A IHP 2.7 104.0 + - - +
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Residues in contact with LYS 24 (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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22A SER* 3.1 6.3 - - - -
23A LYS* 1.3 86.6 - - - +
25A GLU* 1.3 62.7 + - + +
27A GLY* 4.7 0.7 - - - +
28A ALA* 3.3 24.1 + - - +
101A IHP 2.7 69.9 + - - +
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Residues in contact with GLU 25 (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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21A PRO* 3.4 9.9 - - - +
22A SER* 2.7 43.9 + - - +
24A LYS* 1.3 78.5 - - + +
26A ILE* 1.3 59.7 + - - +
28A ALA* 3.3 3.6 + - - +
29A MET* 2.9 31.7 + - - +
69A GLY 5.6 0.3 - - - +
72A LYS* 5.7 7.1 + - - +
73A THR* 3.4 28.9 + - + +
76A LEU* 5.4 1.6 - - - +
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Residues in contact with ILE 26 (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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5A ILE* 3.9 20.2 - - + -
8A ILE* 4.1 29.6 - - + -
9A SER* 4.1 20.6 - - - +
12A CYS* 5.1 0.4 - - - -
21A PRO* 4.2 21.1 - - + +
22A SER 3.1 14.6 + - - +
23A LYS* 3.3 9.8 + - - +
25A GLU* 1.3 75.9 - - - +
27A GLY* 1.3 57.7 + - - +
29A MET* 3.2 6.8 + - + -
30A LEU* 2.9 55.9 + - + +
73A THR* 4.2 16.6 - - + -
77A VAL* 4.7 4.3 - - + -
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Residues in contact with GLY 27 (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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1A SER 5.8 1.8 + - - -
5A ILE* 3.8 23.3 - - - +
23A LYS* 2.8 17.2 + - - -
24A LYS* 4.3 1.3 - - - -
26A ILE* 1.3 77.3 - - - +
28A ALA* 1.3 58.2 + - - +
30A LEU* 3.9 4.1 + - - +
31A SER* 3.1 23.0 + - - -
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Residues in contact with ALA 28 (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 LYS 3.3 19.9 + - - +
25A GLU* 3.8 4.0 - - - +
26A ILE 3.2 0.4 - - - -
27A GLY* 1.3 74.3 - - - +
29A MET* 1.3 65.5 + - - +
31A SER* 3.4 8.8 + - - -
32A LEU* 3.4 19.4 + - - +
70A GLU* 5.9 0.2 - - - -
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Residues in contact with MET 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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25A GLU 2.9 16.8 + - - +
26A ILE* 3.8 3.6 - - + +
28A ALA* 1.3 74.4 - - - +
30A LEU* 1.3 84.4 + - + +
32A LEU* 3.0 17.5 + - + +
33A LEU* 3.1 21.4 + - + +
45A LEU* 6.4 0.2 - - + -
58A LEU* 5.5 2.2 - - + -
70A GLU* 3.3 48.2 - - + +
73A THR* 3.8 20.2 - - + -
74A TRP* 3.4 38.4 - - + +
77A VAL* 4.4 12.3 - - + -
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Residues in contact with LEU 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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1A SER* 3.2 28.7 - - - +
4A VAL* 4.6 9.0 - - + -
5A ILE* 3.8 20.2 - - + -
8A ILE* 6.4 0.9 - - + -
26A ILE* 2.9 39.2 + - + +
27A GLY* 4.0 5.4 - - - +
28A ALA 3.3 0.2 - - - -
29A MET* 1.3 90.2 - - + +
31A SER* 1.3 61.4 + - - +
33A LEU* 3.2 27.4 + - + +
34A GLN* 3.3 19.0 + - - +
42A PRO* 4.0 22.7 - - + +
45A LEU* 5.3 8.3 - - + -
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Residues in contact with SER 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 GLY 3.1 16.1 + - - -
28A ALA* 3.4 8.7 + - - -
29A MET 3.2 0.4 - - - -
30A LEU* 1.3 77.6 - - - +
32A LEU* 1.3 58.7 + - - +
34A GLN* 3.4 13.6 + - - +
35A LYS* 2.9 31.5 + - - +
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Residues in contact with LEU 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 ALA 3.4 8.3 + - - +
29A MET* 3.0 13.8 + - + +
31A SER* 1.3 77.6 - - - +
33A LEU* 1.3 65.3 + - + +
35A LYS* 3.3 26.4 - - + +
36A GLU* 3.0 47.1 + - + +
38A LEU* 6.4 0.4 - - + -
58A LEU* 6.1 1.6 - - + -
61A ARG* 3.7 24.7 - - - +
70A GLU* 3.9 31.2 - - + +
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Residues in contact with LEU 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 MET* 3.1 28.4 + - + +
30A LEU* 3.2 23.5 + - + +
32A LEU* 1.3 77.7 - - + +
34A GLN* 1.3 59.3 + - + +
36A GLU 3.7 0.3 + - - -
37A GLY 3.5 1.6 + - - -
38A LEU* 2.9 50.9 + - + +
39A LEU* 3.3 16.0 + - + -
45A LEU* 4.0 26.0 - - + -
54A ILE* 3.5 36.8 - - + -
58A LEU* 5.3 4.9 - - + -
74A TRP* 4.5 9.0 - - + -
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Residues in contact with GLN 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 LEU* 3.3 16.2 + - - +
31A SER* 3.7 13.4 + - - +
32A LEU 3.2 0.4 - - - -
33A LEU* 1.3 80.3 - - + +
35A LYS* 1.3 61.8 + - - +
37A GLY* 2.9 20.3 + - - -
39A LEU* 3.4 21.2 - - + +
40A MET 3.2 22.7 + - - +
41A SER* 5.0 2.5 - - - -
42A PRO* 3.5 28.5 - - + +
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Residues in contact with LYS 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 SER 2.9 15.8 + - - +
32A LEU* 3.3 42.7 - - + +
34A GLN* 1.3 76.2 - - - +
36A GLU* 1.3 85.6 + - - +
37A GLY 3.4 0.7 + - - -
61A ARG* 5.3 4.1 - - - +
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Residues in contact with GLU 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 LEU* 3.0 37.8 + - + +
33A LEU 4.1 0.2 - - - +
34A GLN 3.1 0.2 - - - -
35A LYS* 1.3 100.7 + - - +
37A GLY* 1.3 62.2 + - - +
38A LEU* 3.4 27.2 + - + +
61A ARG* 4.3 18.4 + - - +
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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