Contacts of the helix formed by residues 28 - 41 (chain A) in PDB entry 4I7H
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 THR 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ARG* 4.0 18.9 - - + +
27A ILE* 1.3 78.9 - - - +
29A GLU* 1.3 76.3 + - - +
30A THR* 2.9 23.9 + - - +
31A ARG* 3.2 33.3 + - + +
32A LYS* 3.1 25.4 + - - +
69A ASN* 4.6 3.8 - - - +
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Residues in contact with GLU 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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28A THR* 1.3 82.2 + - - +
30A THR* 1.3 56.7 + - + +
32A LYS* 3.3 36.1 + - - +
33A ALA* 3.0 27.4 + - - +
58A PHE* 4.2 14.4 - - + -
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Residues in contact with THR 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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28A THR* 2.9 20.1 + - - +
29A GLU* 1.3 73.0 - - + +
31A ARG* 1.3 63.6 + - - +
33A ALA* 3.1 4.9 + - - +
34A ILE* 2.9 33.8 + - - +
58A PHE* 3.4 32.3 - - + -
60A ASN* 3.7 17.7 - - - +
61A MET* 4.2 19.7 - - + -
65A THR* 5.4 3.8 + - - +
69A ASN* 4.0 13.2 + - - -
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Residues in contact with ARG 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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20A LEU* 3.9 16.2 - - - -
25A ILE* 3.4 20.8 - - - +
26A ARG* 3.0 31.1 + - - +
27A ILE* 4.4 4.7 - - + +
28A THR* 3.2 23.9 - - + +
30A THR* 1.3 80.5 + - - +
32A LYS* 1.3 56.1 + - - +
34A ILE* 3.3 3.6 + - - +
35A ILE* 2.9 49.7 + - + +
68A ASN* 5.0 0.8 + - - +
69A ASN* 2.8 40.8 + - + +
72A VAL* 3.6 35.4 - - - +
73A LEU* 5.1 6.3 - - + -
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Residues in contact with LYS 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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13A TYR* 3.5 30.3 - - - +
17A LEU* 4.4 12.8 - - + -
21A ARG* 4.5 11.6 - - - +
27A ILE* 3.7 28.9 + - + -
28A THR 3.1 17.7 + - - +
29A GLU* 3.3 35.1 + - - +
31A ARG* 1.3 77.2 - - - +
33A ALA* 1.3 57.4 + - - +
35A ILE* 3.4 8.3 + - - +
36A SER* 3.0 30.7 + - - -
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Residues in contact with ALA 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 GLU 3.0 13.4 + - - +
30A THR* 3.1 8.5 + - - +
32A LYS* 1.3 77.7 - - - +
34A ILE* 1.3 56.2 + - - +
36A SER* 3.6 5.5 + - - -
37A TYR* 3.0 28.9 + - - +
54A LEU* 3.9 16.8 - - + +
58A PHE* 3.6 29.8 - - + -
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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 THR* 2.9 20.3 + - - +
31A ARG* 3.8 4.5 - - - +
33A ALA* 1.3 74.6 - - - +
35A ILE* 1.3 65.9 + - - +
37A TYR* 3.3 2.9 + - - +
38A MET* 2.9 27.2 + - + +
50A ILE* 4.4 10.5 - - + -
54A LEU* 3.7 21.1 - - + -
61A MET* 4.6 9.2 - - + -
65A THR 4.9 0.2 - - - -
66A VAL* 4.1 24.5 - - + -
69A ASN* 3.6 35.4 - - + +
70A LEU* 4.3 18.8 - - + -
73A LEU* 4.1 18.8 - - + -
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Residues in contact with ILE 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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13A TYR* 4.1 10.8 - - + +
16A VAL* 3.7 35.2 - - + -
17A LEU* 3.7 27.1 - - + -
20A LEU* 4.2 4.5 - - + -
31A ARG* 2.9 39.3 + - + +
32A LYS* 3.6 5.2 - - - +
34A ILE* 1.3 77.2 - - - +
36A SER* 1.3 56.8 + - - +
38A MET* 3.2 3.6 + - - +
39A ILE* 3.0 49.2 + - + +
73A LEU* 3.9 26.7 - - + -
94A PHE* 4.8 4.2 - - + -
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Residues in contact with SER 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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13A TYR* 4.1 19.0 - - - -
32A LYS 3.0 17.3 + - - -
33A ALA* 3.8 6.7 - - - -
35A ILE* 1.3 74.2 - - - +
37A TYR* 1.3 65.9 + - - +
39A ILE* 3.2 5.9 + - - +
40A GLN* 3.0 39.5 + - - +
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Residues in contact with TYR 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 ALA 3.0 19.4 + - - +
34A ILE* 3.6 7.4 - - - +
36A SER* 1.3 74.3 - - - +
38A MET* 1.3 68.3 + - - +
40A GLN* 3.2 4.7 + - - -
41A SER* 3.0 27.6 + - - -
45A PRO* 4.0 15.0 - - + +
49A LYS* 3.3 20.4 - - - +
50A ILE* 3.6 37.2 - - + -
53A ASP* 2.6 41.7 + - + -
54A LEU* 4.1 22.7 - - + -
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Residues in contact with MET 38 (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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34A ILE* 2.9 25.6 + - + +
35A ILE* 3.6 5.8 - - - +
37A TYR* 1.3 75.8 - - - +
39A ILE* 1.3 61.3 + - - +
41A SER* 2.9 21.2 + - - +
45A PRO* 3.7 16.2 - - + -
50A ILE* 3.7 26.5 - - + -
70A LEU* 4.3 14.4 - - + -
73A LEU* 5.1 1.8 - - + -
79A VAL* 4.6 11.4 - - + -
92A TYR* 3.7 32.3 - - + +
93A ASP 3.8 1.6 - - - -
94A PHE* 3.5 52.8 - - + +
119A MET* 5.5 0.2 - - - +
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Residues in contact with ILE 39 (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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12A ALA* 3.8 13.2 - - + -
13A TYR* 3.3 45.3 - - + +
35A ILE* 3.0 28.8 + - + +
36A SER* 3.2 8.5 + - - +
38A MET* 1.3 79.3 - - - +
40A GLN* 1.3 79.1 + - - +
41A SER 3.6 3.6 + - - +
94A PHE* 3.6 30.5 - - + -
119A MET* 3.5 28.1 - - + +
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Residues in contact with GLN 40 (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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13A TYR* 6.4 0.2 - - - +
36A SER* 3.0 27.1 + - - +
37A TYR* 3.7 4.7 - - - +
39A ILE* 1.3 92.9 - - - +
41A SER* 1.3 64.1 + - - +
42A THR* 3.6 11.4 + - - +
132A LYS* 5.1 11.2 - - + +
133A VAL 3.2 24.7 - - - +
134A THR* 3.9 19.0 + - - +
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Residues in contact with SER 41 (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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37A TYR* 3.0 21.4 + - - -
38A MET* 2.9 22.9 + - - +
39A ILE 3.4 5.0 - - - +
40A GLN* 1.3 79.3 - - - +
42A THR* 1.3 61.7 + - - +
43A GLU 3.5 18.4 + - - -
45A PRO* 4.0 18.4 - - - +
94A PHE 5.6 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
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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