Contacts of the helix formed by residues 4 - 18 (chain B) in PDB entry 3PSR
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 GLN 4 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B THR* 1.3 73.5 - - - +
5B ALA* 1.3 62.0 + - - +
7B ARG* 3.0 43.0 + - - +
8B SER* 3.0 26.5 + - - -
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Residues in contact with ALA 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A MET* 4.6 7.2 - - + +
15A MET* 4.0 13.0 - - + -
38A ASN* 3.5 39.2 + - + +
39A PHE* 4.0 15.6 - - + -
3B THR* 3.1 1.9 + - - +
4B GLN* 1.3 79.7 - - - +
6B GLU* 1.3 64.6 + - - +
8B SER* 3.2 7.5 + - - -
9B ILE* 3.1 23.7 + - - +
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Residues in contact with GLU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASN 3.7 9.0 - - - +
39A PHE* 3.2 23.0 - - + -
40A PRO* 3.9 1.3 - - - -
41A ASN* 2.5 55.0 + - - -
42A PHE 3.3 6.8 + - - -
85A TYR* 3.5 21.7 - - + +
2B ASN* 3.5 10.6 - - - +
3B THR* 3.0 32.4 + - - +
5B ALA* 1.3 77.0 - - - +
7B ARG* 1.3 64.3 + - - +
9B ILE* 2.9 10.0 + - - +
10B ILE* 2.9 27.1 + - + +
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Residues in contact with ARG 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ASN* 3.0 41.3 + - + +
3B THR* 3.0 10.1 + - - +
4B GLN* 3.0 58.5 + - - +
6B GLU* 1.3 76.8 - - - +
8B SER* 1.3 57.2 + - - +
10B ILE* 3.1 11.6 + - + +
11B GLY* 2.8 28.9 + - - -
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Residues in contact with SER 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER* 2.8 33.6 + - - -
12A MET* 3.9 20.5 - - - +
4B GLN* 3.0 19.5 + - - -
5B ALA* 3.4 8.5 - - - -
6B GLU 3.1 0.2 - - - -
7B ARG* 1.3 78.1 - - - +
9B ILE* 1.3 60.0 + - - +
11B GLY* 3.4 2.7 + - - -
12B MET* 3.2 24.1 + - - +
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Residues in contact with ILE 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A MET* 4.9 10.5 - - - -
39A PHE* 4.2 11.9 - - + -
78A LEU* 4.0 16.8 - - + +
81A ILE* 3.7 27.4 - - + -
82A ALA* 3.7 25.7 - - + +
85A TYR* 3.7 28.3 - - + -
5B ALA 3.1 13.6 + - - +
6B GLU* 2.9 10.4 + - - +
8B SER* 1.3 74.1 - - - +
10B ILE* 1.3 69.0 + - - +
12B MET* 2.9 30.8 + - + +
13B ILE* 3.2 11.6 + - + +
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Residues in contact with ILE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A TYR* 4.1 31.2 - - + -
2B ASN* 4.0 25.8 - - - +
6B GLU* 2.9 25.7 + - + +
7B ARG* 3.6 9.4 - - + +
9B ILE* 1.3 76.9 - - - +
11B GLY* 1.3 59.3 + - - +
13B ILE* 2.9 12.7 + - + +
14B ASP* 2.8 42.7 + - - +
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Residues in contact with GLY 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLN* 5.9 2.2 - - - -
7B ARG 2.8 16.1 + - - -
8B SER 3.7 3.1 - - - -
9B ILE 3.1 0.4 - - - -
10B ILE* 1.3 78.8 - - - +
12B MET* 1.3 55.8 + - - +
14B ASP* 3.0 11.2 + - - +
15B MET* 2.8 31.1 + - - +
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Residues in contact with MET 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER* 4.8 8.7 - - - +
9A ILE* 6.4 1.8 - - + -
12A MET* 4.7 12.1 - - - +
78A LEU* 6.0 3.8 - - + +
82A ALA* 4.7 17.7 - - + -
8B SER* 3.2 25.1 + - - +
9B ILE* 2.9 27.7 + - + +
11B GLY* 1.3 76.1 - - - +
13B ILE* 1.3 60.0 + - + +
15B MET* 3.4 9.1 + - - +
16B PHE* 2.9 27.4 + - - +
71B PHE* 5.9 0.9 - - + -
74B PHE* 3.7 11.1 - - + -
75B LEU* 4.7 10.3 - - + -
78B LEU* 4.5 28.9 - - + -
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA* 3.4 14.6 - - + +
85A TYR* 3.4 15.9 - - + -
86A HIS* 3.1 39.7 - - + +
89A SER* 4.4 11.9 - - - +
9B ILE* 3.2 11.8 + - + +
10B ILE* 2.9 11.7 + - + +
12B MET* 1.3 76.0 - - + +
14B ASP* 1.3 70.6 + - - +
16B PHE* 3.2 8.9 + - - +
17B HIS* 3.1 42.4 + - + +
71B PHE* 4.0 18.6 - - + -
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Residues in contact with ASP 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 2.8 33.6 + - - +
11B GLY* 3.0 12.1 + - - +
13B ILE* 1.3 80.9 - - - +
15B MET* 1.3 66.7 + - - +
17B HIS* 3.2 8.1 + - - +
18B LYS* 3.2 20.0 + - - +
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Residues in contact with MET 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ALA* 4.1 14.4 - - - -
11B GLY 2.8 19.5 + - - +
12B MET* 3.5 6.7 - - + +
14B ASP* 1.3 70.7 - - - +
16B PHE* 1.3 65.1 + - - +
18B LYS* 3.1 25.6 + - + +
19B TYR* 3.1 19.1 - - + -
34B MET* 3.8 17.0 - - + -
38B ASN* 3.8 37.7 - - - +
39B PHE* 4.5 9.0 - - + -
74B PHE* 3.3 42.0 - - + -
78B LEU* 4.5 7.2 - - + -
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Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A HIS* 4.4 2.9 - - - -
12B MET 2.9 14.4 + - - +
13B ILE* 3.2 12.3 - - - +
14B ASP 3.2 0.2 - - - -
15B MET* 1.3 76.7 - - - +
17B HIS* 1.3 81.5 + + - +
18B LYS 3.0 5.7 + - - -
19B TYR* 3.1 17.6 + - - +
20B THR* 3.8 23.2 + - + +
24B ASP 4.0 14.4 - - - -
26B ILE* 3.7 23.0 - - + +
34B MET* 5.7 0.4 - - - -
69B ILE 4.1 7.4 - - - -
70B ASP 3.9 2.5 - - - -
71B PHE* 3.5 41.5 - + + -
74B PHE* 3.3 54.5 - + + -
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Residues in contact with HIS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A HIS* 3.7 16.6 + + - -
89A SER* 3.5 17.6 - - - -
90A HIS* 3.0 35.3 + + - -
13B ILE* 3.1 22.4 + - + +
14B ASP* 3.2 5.9 + - - +
16B PHE* 1.3 93.6 - + - +
18B LYS* 1.3 61.5 + - - +
19B TYR 3.0 0.4 - - - -
20B THR* 2.7 29.8 + - + +
21B ARG 4.6 4.0 + - - +
23B ASP 5.0 3.8 - - - -
24B ASP* 5.2 1.3 - - - -
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Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASP 3.2 9.6 + - - +
15B MET* 3.1 21.2 + - + +
16B PHE 3.0 0.6 + - - -
17B HIS* 1.3 78.7 - - - +
19B TYR* 1.3 90.3 + - + +
20B THR 3.5 0.4 + - - -
21B ARG 4.7 2.8 + - - -
37B GLU* 3.8 9.8 + - - +
38B ASN* 5.0 6.7 + - - -
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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