Contacts of the helix formed by residues 31 - 49 (chain A) in PDB entry 4H7Y
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 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PRO 3.6 2.5 + - - -
30A LEU* 1.3 75.3 - - - +
32A ASP* 1.3 60.0 + - - +
33A ALA* 3.5 9.7 + - - +
34A LEU* 3.1 31.4 + - - +
35A LEU* 2.8 29.3 + - - +
66B ARG* 4.8 5.8 - - - +
69B GLU* 5.1 14.6 - - - -
73B ILE* 3.7 8.0 - - - +
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Residues in contact with ASP 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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31A SER* 1.3 72.7 - - - +
33A ALA* 1.3 59.5 + - - +
35A LEU* 3.3 5.8 + - - +
36A ASN* 2.9 53.9 + - - +
74A GLN* 5.9 1.2 - - - +
69B GLU* 5.0 1.8 + - - +
72B ALA* 4.7 11.0 - - + +
73B ILE* 3.5 31.1 - - + +
76B PRO* 6.2 0.2 - - - +
106B SER* 4.1 22.6 - - - +
107B GLN* 6.3 0.9 - - - -
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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
----------------------------------------------------------
31A SER* 3.1 9.2 + - - +
32A ASP* 1.3 82.2 + - - +
34A LEU* 1.3 65.5 + - + +
36A ASN* 3.4 8.0 + - - +
37A LYS* 3.1 22.2 + - - +
102B GLN* 5.1 6.5 - - + +
144B GLN* 3.9 37.5 + - + +
52D ASP* 4.7 3.5 - - - +
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 3.2 35.9 + - - +
29A PRO 3.7 11.9 - - - +
30A LEU* 3.8 15.1 - - + +
31A SER* 3.1 21.0 + - - +
33A ALA* 1.3 76.9 - - + +
35A LEU* 1.3 61.3 + - - +
37A LYS* 3.4 30.9 + - + +
38A LEU* 3.0 28.8 + - - +
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Residues in contact with LEU 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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30A LEU* 4.2 10.0 - - + +
31A SER 2.8 17.2 + - - +
32A ASP* 3.7 7.0 - - - +
34A LEU* 1.3 75.4 - - - +
36A ASN* 1.3 62.2 + - - +
38A LEU* 3.2 11.8 + - + +
39A ILE* 2.9 44.2 + - + +
70A LEU* 3.6 31.0 - - + -
73A ILE* 3.8 17.9 - - + -
74A GLN* 4.8 7.9 - - + -
30B LEU* 4.7 12.6 - - + -
73B ILE* 3.7 32.3 - - + -
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Residues in contact with ASN 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP* 2.9 45.1 + - - +
33A ALA* 3.7 7.6 - - - +
35A LEU* 1.3 77.3 - - - +
37A LYS* 1.3 57.6 + - - +
39A ILE* 3.4 2.0 + - - +
40A GLY* 2.9 23.9 + - - -
74A GLN* 2.9 36.5 + - - +
52D ASP* 3.6 22.8 - - + +
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Residues in contact with LYS 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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23A LEU* 3.9 31.9 - - + +
27A SER* 4.0 6.9 + - - -
33A ALA 3.1 16.6 + - - +
34A LEU* 3.7 32.2 + - + +
36A ASN* 1.3 77.6 - - - +
38A LEU* 1.3 58.4 + - - +
40A GLY* 3.3 2.6 + - - -
41A ARG* 3.0 27.8 + - + +
50D PRO* 6.1 2.0 - - + -
52D ASP* 3.7 28.7 - - - +
53D LYS* 6.2 1.8 - - - +
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Residues in contact with LEU 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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20A LEU* 3.9 15.7 - - + +
23A LEU* 3.9 26.5 - - + -
24A GLU* 3.7 42.4 - - + +
27A SER* 5.7 1.8 - - - +
30A LEU* 5.0 8.7 - - + -
34A LEU 3.0 18.0 + - - +
35A LEU* 3.2 11.0 + - + +
37A LYS* 1.3 77.6 - - - +
39A ILE* 1.3 61.2 + - - +
41A ARG* 3.2 3.6 + - - +
42A TYR* 3.0 51.7 + - + -
70A LEU* 4.0 21.1 - - + -
30B LEU* 6.2 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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35A LEU* 2.9 31.3 + - + +
36A ASN 3.8 4.5 - - - +
38A LEU* 1.3 75.2 - - - +
40A GLY* 1.3 63.2 + - - +
42A TYR* 3.3 9.2 + - - +
43A SER* 3.0 18.5 + - - -
67A PHE* 3.7 23.8 - - + -
70A LEU* 3.7 34.8 - - + +
71A LYS* 3.8 15.7 - - + +
74A GLN* 3.5 48.2 - - + +
89D ASN* 5.6 4.0 - - - +
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Residues in contact with GLY 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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36A ASN 2.9 15.8 + - - -
37A LYS 3.6 4.0 - - - -
39A ILE* 1.3 78.2 - - - +
41A ARG* 1.3 59.5 + - - +
43A SER* 2.6 23.6 + - - -
44A GLN* 3.1 6.4 + - - +
51D PRO* 3.5 36.2 - - - +
52D ASP* 4.8 2.5 - - - -
89D ASN* 4.9 1.8 - - - -
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Residues in contact with ARG 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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16A TRP* 3.6 15.7 - - + -
19A LEU* 3.9 29.5 - - + +
20A LEU* 3.7 19.9 - - + +
23A LEU* 3.8 22.9 - - + +
37A LYS* 3.0 14.5 + - - +
38A LEU 3.2 8.0 + - - +
40A GLY* 1.3 73.9 - - - +
42A TYR* 1.3 65.2 + - - +
44A GLN* 2.9 42.0 + - - +
45A ALA* 3.0 10.6 + - - +
47D GLU* 2.8 40.1 + - - -
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Residues in contact with TYR 42 (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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17A LEU* 4.7 3.3 - - + +
20A LEU* 3.6 46.7 + - + +
21A LEU* 4.4 8.8 - - - +
24A GLU* 4.6 4.3 + - - -
38A LEU* 3.0 44.9 + - + -
39A ILE* 3.3 8.5 + - - +
41A ARG* 1.3 75.2 - - - +
43A SER* 1.3 63.7 + - - +
45A ALA* 3.1 4.9 + - - +
46A ILE* 3.0 24.8 + - - +
63A ILE* 3.6 27.1 - - + -
66A ARG* 3.4 40.0 - - + +
67A PHE* 3.6 21.8 - + + -
70A LEU* 3.7 21.1 - - + -
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Residues in contact with SER 43 (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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39A ILE 3.0 12.4 + - - -
40A GLY 2.6 19.1 + - - -
42A TYR* 1.3 76.8 - - - +
44A GLN* 1.3 57.3 + - - +
46A ILE* 3.1 3.1 + - - +
47A GLU* 2.9 33.8 + - - +
67A PHE* 4.1 7.1 - - - -
51D PRO* 3.5 7.1 - - - +
85D MET* 3.7 25.0 - - - +
89D ASN* 3.1 34.9 + - - -
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Residues in contact with GLN 44 (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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16A TRP* 4.1 4.4 - - - -
40A GLY 3.1 6.4 + - - +
41A ARG* 2.9 54.6 + - - +
43A SER* 1.3 82.4 + - - +
45A ALA* 1.3 60.2 + - - +
47A GLU* 3.4 11.1 + - - +
48A ALA* 3.3 21.1 + - - +
46D ILE* 3.0 33.6 + - + +
47D GLU* 3.3 24.7 + - - +
49D LEU 3.5 17.0 + - - -
50D PRO* 4.1 4.6 - - - +
51D PRO* 3.7 18.9 - - + +
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Residues in contact with ALA 45 (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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16A TRP* 3.4 41.6 - - + -
20A LEU* 3.8 19.7 - - + -
41A ARG 3.0 6.2 + - - +
42A TYR 3.1 9.2 + - - +
44A GLN* 1.3 77.4 - - - +
46A ILE* 1.3 62.7 + - - +
48A ALA* 3.0 10.9 + - - +
49A LEU* 3.2 22.2 + - + +
63A ILE* 4.3 8.3 - - + -
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Residues in contact with ILE 46 (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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42A TYR 3.0 12.1 + - - +
43A SER 3.1 6.7 + - - +
45A ALA* 1.3 76.2 - - - +
47A GLU* 1.3 61.9 + - - +
48A ALA 3.3 0.7 + - - -
49A LEU* 3.5 19.5 + - - +
60A PHE* 5.4 2.2 - - + -
63A ILE* 4.0 15.7 - - + -
64A GLN* 3.8 29.2 - - + +
67A PHE* 3.8 40.8 - - + -
85A MET* 4.0 11.4 - - + -
81D ASP* 4.1 15.8 - - + +
82D TYR* 3.8 8.7 - - - -
85D MET* 3.8 29.2 - - + -
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Residues in contact with GLU 47 (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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43A SER* 2.9 23.9 + - - +
44A GLN* 3.6 6.5 - - - +
45A ALA 3.2 0.4 - - - -
46A ILE* 1.3 78.0 - - - +
48A ALA* 1.3 59.0 + - + +
43D SER* 5.1 1.4 + - - -
46D ILE* 3.8 33.6 - - + +
64D GLN* 3.7 27.5 + - - +
67D PHE* 3.6 28.1 - - + -
71D LYS* 5.3 1.0 + - - -
82D TYR* 3.4 43.1 + - - +
85D MET* 3.5 25.1 - - + +
89D ASN* 5.6 0.2 - - - +
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Residues in contact with ALA 48 (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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11A ASN* 2.8 46.2 + - - +
16A TRP* 4.0 15.5 - - + +
44A GLN 3.3 14.4 + - - +
45A ALA 3.0 7.1 + - - +
47A GLU* 1.3 79.6 - - - +
49A LEU* 1.3 58.6 + - - +
50A PRO* 3.5 7.3 - - - +
43D SER* 6.0 2.0 - - - -
47D GLU* 5.9 0.4 - - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 3.9 12.1 - - - +
12A ASN* 3.7 27.8 - - - -
13A PRO* 3.7 8.1 - - + -
16A TRP* 3.8 20.6 - - + -
45A ALA 3.2 20.7 + - - +
46A ILE 3.5 10.4 + - - +
47A GLU 3.5 1.6 - - - -
48A ALA* 1.3 78.5 - - - +
50A PRO* 1.3 69.0 - - + +
51A PRO* 3.3 5.5 - - - +
54A TYR* 3.8 16.6 - - + -
60A PHE* 3.6 31.5 - - + -
63A ILE* 3.7 29.8 - - + -
81D ASP* 4.8 0.5 - - - +
82D TYR* 4.4 1.9 + - - -
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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
------------------------------------------------------------
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