Contacts of the helix formed by residues 40 - 59 (chain A) in PDB entry 6PSI
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ASN* 2.9 29.3 + - - -
39A LYS* 1.3 76.4 + - - +
41A PRO* 1.4 60.5 - - - -
42A GLU* 3.3 4.5 - - - -
43A ALA* 2.8 34.3 + - - +
44A GLU* 3.2 11.9 + - - +
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Residues in contact with PRO 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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39A LYS 4.4 3.4 - - - +
40A SER* 1.4 79.2 - - - +
42A GLU* 1.3 57.1 + - - +
44A GLU* 3.0 18.4 + - + +
45A GLU* 2.9 43.2 + - + +
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Residues in contact with GLU 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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40A SER* 3.0 5.5 + - - +
41A PRO* 1.3 75.5 - - - +
43A ALA* 1.3 58.5 + - - +
45A GLU* 4.1 4.8 - - - +
46A LYS* 3.1 45.8 + - + +
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Residues in contact with ALA 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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33A TYR* 3.7 26.3 - - + +
38A ASN* 3.4 33.0 - - - +
40A SER* 2.8 16.3 + - - +
42A GLU* 1.3 76.9 - - - +
44A GLU* 1.3 57.7 + - - +
46A LYS* 3.9 5.9 - - - +
47A PHE* 3.0 27.6 + - - +
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Residues in contact with GLU 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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35A PRO* 3.6 36.5 - - + +
38A ASN 4.0 3.6 - - - +
39A LYS* 3.7 7.9 - - - +
40A SER 3.4 22.9 + - - +
41A PRO* 3.0 32.4 + - + +
43A ALA* 1.3 76.8 - - - +
45A GLU* 1.3 66.8 + - - +
46A LYS 3.3 0.2 - - - -
47A PHE* 3.4 8.3 + - - +
48A LYS* 3.0 33.9 + - + +
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Residues in contact with GLU 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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41A PRO* 2.9 27.1 + - + +
42A GLU* 4.1 4.9 - - - +
44A GLU* 1.3 76.8 - - - +
46A LYS* 1.3 65.4 + - - +
48A LYS* 3.0 40.5 + - - +
49A GLU* 3.0 29.1 + - - +
92A ASP* 3.5 14.5 - - - +
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Residues in contact with LYS 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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10A ILE* 5.6 5.1 - - + +
33A TYR* 4.6 15.0 - - + -
42A GLU* 3.1 33.0 + - + +
43A ALA* 3.9 7.2 - - - +
45A GLU* 1.3 77.3 - - - +
47A PHE* 1.3 62.1 + - - +
49A GLU* 3.0 35.2 + - + +
50A ILE* 3.0 39.2 + - + +
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Residues in contact with PHE 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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26A TYR* 4.0 14.1 - + - -
29A LEU 3.9 11.0 - - - -
30A ALA* 3.6 32.3 - - + -
33A TYR* 3.7 17.9 - - + +
34A HIS* 5.9 0.7 - - - -
35A PRO* 3.6 32.5 - - + -
43A ALA 3.0 22.0 + - - +
44A GLU* 3.4 9.6 - - - +
45A GLU 3.3 0.2 - - - -
46A LYS* 1.3 75.3 - - - +
48A LYS* 1.3 61.7 + - + +
50A ILE* 3.1 16.2 + - + +
51A ASN* 2.9 59.5 + - - -
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Residues in contact with LYS 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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44A GLU 3.0 14.9 + - - +
45A GLU* 3.0 43.3 + - - +
47A PHE* 1.3 79.7 - - + +
49A GLU* 1.3 51.8 + - - +
51A ASN* 3.2 9.3 + - + +
52A GLU 2.8 27.5 + - - -
89A ASP* 2.9 34.6 + - + +
92A ASP* 2.9 29.5 + - - -
93A PHE* 3.1 28.1 - - + -
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Residues in contact with GLU 49 (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 LYS* 3.2 33.0 + - - +
10A ILE* 3.3 24.7 - - + +
45A GLU* 3.0 16.5 + - - +
46A LYS* 3.0 44.5 + - + +
48A LYS* 1.3 76.3 - - + +
50A ILE* 1.3 58.3 + - - +
52A GLU* 3.2 10.5 - - - +
53A ALA* 2.9 23.7 + - - +
93A PHE* 5.4 3.8 - - + -
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Residues in contact with ILE 50 (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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10A ILE* 3.8 25.4 - - + +
11A LEU* 3.5 16.9 - - + +
26A TYR* 3.6 23.6 - - + +
29A LEU* 3.7 29.8 - - + +
33A TYR* 3.6 32.5 - - + -
46A LYS* 3.2 22.2 - - + +
47A PHE* 3.2 20.2 - - + +
49A GLU* 1.3 76.2 - - - +
51A ASN* 1.3 55.6 + - - +
54A TYR* 3.0 29.1 + - - +
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Residues in contact with ASN 51 (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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26A TYR* 2.9 27.2 + - - -
47A PHE* 2.9 58.3 + - - +
48A LYS* 3.2 13.0 + - - +
50A ILE* 1.3 74.8 - - - +
52A GLU* 1.3 57.6 + - - +
54A TYR* 4.2 4.9 - - - -
55A ALA* 2.9 28.7 + - - +
88A PHE* 3.1 38.3 - - + -
93A PHE* 4.4 4.5 - - + -
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Residues in contact with GLU 52 (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 LYS* 2.9 31.5 + - - +
7A TYR* 3.4 26.5 - - + +
10A ILE* 3.6 9.4 - - - +
48A LYS 2.8 9.2 + - - +
49A GLU* 3.2 11.2 - - - +
51A ASN* 1.3 74.1 - - - +
53A ALA* 1.3 64.0 + - - +
55A ALA* 3.2 7.2 - - - +
56A VAL* 3.2 28.8 + - + +
85A PHE* 4.4 2.5 - - + -
93A PHE* 3.5 32.4 - - + +
94A SER* 3.1 36.7 + - - -
97A PHE* 4.7 6.1 - - + -
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Residues in contact with ALA 53 (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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7A TYR* 3.3 47.1 - - + +
10A ILE* 4.0 6.7 - - + -
11A LEU* 3.7 14.4 - - + -
49A GLU 2.9 15.4 + - - +
50A ILE 3.7 2.5 - - - +
52A GLU* 1.3 78.7 - - - +
54A TYR* 1.3 56.4 + - - +
56A VAL* 3.5 2.1 + - - +
57A LEU* 3.0 35.4 + - - +
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Residues in contact with TYR 54 (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 LEU* 4.3 6.8 - - + +
19A GLN* 5.4 7.1 + - - -
22A ILE* 4.2 17.0 - - + -
23A LYS* 5.0 11.5 - - + +
26A TYR* 3.7 58.5 - + + -
50A ILE 3.0 20.3 + - - +
51A ASN* 4.2 1.8 - - - -
53A ALA* 1.3 73.2 - - - +
55A ALA* 1.4 58.2 + - - +
57A LEU* 4.4 2.0 - - - +
58A SER* 2.7 66.2 + - - -
88A PHE* 4.3 19.5 - + - -
146A SER 5.0 5.4 + - - -
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Residues in contact with ALA 55 (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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51A ASN 2.9 23.5 + - - +
52A GLU 3.2 8.3 + - - +
54A TYR* 1.4 77.1 - - - +
56A VAL* 1.3 63.5 + - - +
58A SER* 3.8 3.7 + - - -
59A ASP* 3.7 6.6 - - - +
62A LYS* 2.9 24.0 + - - +
85A PHE* 3.3 29.6 - - + -
88A PHE* 3.4 25.5 - - + -
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Residues in contact with VAL 56 (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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7A TYR* 3.7 27.6 - - + +
52A GLU* 3.2 14.2 + - + +
53A ALA 3.9 5.4 - - - +
55A ALA* 1.3 78.1 - - + +
57A LEU* 1.3 62.0 + - + +
58A SER 3.4 1.5 + - - -
59A ASP 3.7 1.2 + - - +
62A LYS* 3.1 36.1 - - - +
63A ARG 2.9 24.9 + - - -
66A TYR* 3.7 21.5 - - + -
85A PHE* 4.8 7.9 - - + -
97A PHE* 5.1 1.3 - - + -
101A PHE* 3.6 30.5 - - + -
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Residues in contact with LEU 57 (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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7A TYR* 3.6 27.8 - - + -
8A TYR* 4.4 9.0 - - + +
11A LEU* 4.0 7.6 - - + -
19A GLN* 4.3 9.5 - - - +
22A ILE* 3.6 48.1 - - + +
53A ALA 3.0 16.5 + - - +
54A TYR 3.5 1.6 - - - +
56A VAL* 1.3 87.5 - - + +
58A SER* 1.4 60.9 + - - +
59A ASP 3.6 0.7 - - - -
63A ARG* 3.4 47.4 - - - +
66A TYR* 3.6 21.3 - - + -
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Residues in contact with SER 58 (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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19A GLN* 4.3 13.4 + - - +
54A TYR* 2.7 57.4 + - - -
55A ALA* 4.0 6.5 - - - -
56A VAL 3.4 0.8 - - - -
57A LEU* 1.4 75.1 - - - +
59A ASP* 1.3 70.2 + - - +
60A PRO* 4.0 1.0 - - - +
88A PHE* 6.1 0.9 - - - -
143A ARG* 4.9 5.0 + - - -
145A VAL* 5.5 1.6 - - - +
146A SER* 3.7 29.1 + - - -
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Residues in contact with ASP 59 (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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55A ALA 3.7 2.4 - - - +
56A VAL 4.1 1.6 + - - -
58A SER* 1.3 80.5 + - - +
60A PRO* 1.4 59.9 - - - +
61A GLU* 3.3 2.6 + - + +
62A LYS* 3.0 44.9 + - + +
63A ARG* 2.9 34.4 + - - +
84A ASP* 3.5 0.2 - - - +
143A ARG* 2.9 43.5 + - + -
144A ARG 3.8 7.9 - - - +
145A VAL* 3.3 15.8 - - - +
146A SER 4.0 1.1 + - - +
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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