Contacts of the helix formed by residues 4 - 18 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A THR* 1.3 74.7 - - - +
5A ALA* 1.3 52.8 + - - +
7A ARG* 2.9 41.8 + - - +
8A SER* 2.6 51.2 + - - +
11B GLY* 5.9 2.6 - - - -
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Residues in contact with ALA 5 (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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3A THR* 3.2 1.7 + - - +
4A GLN* 1.3 79.0 - - - +
6A GLU* 1.3 64.3 + - - +
8A SER* 3.0 16.9 + - - -
9A ILE* 3.0 17.7 + - - +
15B MET* 4.1 10.8 - - - -
38B ASN* 3.6 41.0 + - + +
39B PHE* 4.0 14.1 - - + -
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Residues in contact with GLU 6 (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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2A ASN* 2.7 27.3 - - - +
3A THR* 2.6 45.3 + - - +
5A ALA* 1.3 77.7 - - - +
7A ARG* 1.3 64.4 + - - +
9A ILE* 3.2 5.4 + - - +
10A ILE* 3.0 29.4 + - + +
38B ASN 3.6 6.3 - - - +
39B PHE* 3.5 16.4 - - + -
40B PRO* 3.4 10.5 - - - +
41B ASN* 2.9 38.6 + - - +
42B PHE 3.4 6.1 + - - -
85B TYR* 3.7 16.9 + - - +
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Residues in contact with ARG 7 (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* 5.6 1.2 + - - -
2A ASN* 3.3 26.1 + - + +
3A THR* 2.9 12.4 + - - +
4A GLN* 3.2 62.7 - - - +
6A GLU* 1.3 77.1 - - - +
8A SER* 1.3 65.0 + - - +
10A ILE* 3.2 11.6 + - + +
11A GLY* 2.9 20.6 + - - -
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Residues in contact with SER 8 (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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4A GLN* 2.6 29.3 + - - +
5A ALA* 3.0 13.4 + - - -
7A ARG* 1.3 74.8 - - - +
9A ILE* 1.3 61.9 + - - +
11A GLY* 3.3 9.7 + - - -
12A MET* 3.5 16.6 + - - +
8B SER* 2.8 41.5 + - - -
12B MET* 4.8 8.2 - - - +
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Residues in contact with ILE 9 (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 ALA 3.0 14.1 + - - +
6A GLU* 3.7 8.5 - - - +
8A SER* 1.3 76.1 - - - +
10A ILE* 1.3 66.5 + - - +
12A MET* 3.0 21.4 + - - +
13A ILE* 3.4 10.8 + - + +
12B MET* 6.4 2.0 - - + -
39B PHE* 3.9 16.8 - - + -
78B LEU* 4.0 20.0 - - + +
81B ILE* 3.6 31.4 - - + -
82B ALA* 3.8 30.6 - - + +
85B TYR* 4.3 17.7 - - + -
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Residues in contact with ILE 10 (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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2A ASN* 4.2 17.3 - - + +
6A GLU 3.0 27.3 + - - +
7A ARG* 3.6 10.5 - - + +
9A ILE* 1.3 77.3 - - - +
11A GLY* 1.3 58.9 + - - +
13A ILE* 3.1 11.8 + - + +
14A ASP* 2.8 46.1 + - - +
85B TYR* 3.8 35.9 - - + -
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Residues in contact with GLY 11 (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 ARG 2.9 13.8 + - - -
8A SER* 3.7 5.8 - - - -
9A ILE 3.1 0.8 - - - -
10A ILE* 1.3 77.9 - - - +
12A MET* 1.3 53.8 + - - +
14A ASP* 3.1 9.9 + - - +
15A MET* 2.6 36.1 + - - +
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Residues in contact with MET 12 (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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8A SER 3.5 13.9 - - - +
9A ILE* 3.0 12.5 + - + +
11A GLY* 1.3 78.3 - - - +
13A ILE* 1.3 59.0 + - + +
15A MET* 3.3 28.8 + - + +
16A PHE* 2.8 28.6 + - - +
39A PHE* 5.3 0.7 - - + -
71A PHE* 5.3 2.0 - - + -
74A PHE* 3.8 8.5 - - + -
75A LEU* 6.2 2.2 - - + -
78A LEU* 3.8 28.3 - - + -
5B ALA* 4.6 12.3 - - + +
8B SER* 3.9 26.5 - - - +
9B ILE* 4.9 8.1 - - + -
12B MET* 4.7 18.4 - - - +
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Residues in contact with ILE 13 (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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9A ILE* 3.4 11.8 + - + +
10A ILE* 3.1 12.2 + - + +
12A MET* 1.3 76.7 - - + +
14A ASP* 1.3 69.4 + - - +
16A PHE* 3.3 8.3 + - - +
17A HIS* 3.0 45.7 + - + +
71A PHE* 3.9 23.8 - - + -
82B ALA* 3.5 7.0 - - + +
85B TYR* 3.3 23.1 - - + +
86B HIS* 3.1 33.9 - - + +
89B SER* 4.2 13.0 - - - +
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Residues in contact with ASP 14 (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* 2.8 35.4 + - - +
11A GLY* 3.4 11.4 - - - +
13A ILE* 1.3 81.5 - - - +
15A MET* 1.3 65.4 + - - +
17A HIS* 3.2 10.1 + - - +
18A LYS* 3.1 32.6 + - - +
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Residues in contact with MET 15 (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 GLY 2.6 17.1 + - - +
12A MET* 3.4 27.1 - - + +
14A ASP* 1.3 72.4 - - - +
16A PHE* 1.3 64.5 + - - +
18A LYS* 2.9 23.3 + - + +
19A TYR* 3.1 34.0 - - + -
34A MET* 4.5 5.6 - - + +
38A ASN* 3.8 29.6 - - - +
39A PHE* 4.1 20.4 - - + -
74A PHE* 3.7 29.6 - - + -
78A LEU* 4.2 2.9 - - + -
5B ALA* 4.0 14.4 - - - -
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Residues in contact with PHE 16 (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 MET 2.8 17.4 + - - +
13A ILE* 3.3 11.7 - - - +
15A MET* 1.3 73.5 - - - +
17A HIS* 1.3 70.6 + + - +
19A TYR* 2.9 22.5 + - - +
20A THR* 3.2 30.6 + - + +
24A ASP* 3.3 31.6 - - - -
26A ILE* 3.6 27.3 - - + +
34A MET* 5.9 0.2 - - - -
69A ILE 4.1 3.1 - - - -
70A ASP 3.9 4.0 - - - -
71A PHE* 3.6 29.4 - + + -
74A PHE* 3.5 48.0 - + + -
103A ZN 4.0 4.5 - - - -
86B HIS* 4.1 7.2 - + - -
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Residues in contact with HIS 17 (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 ILE* 3.0 23.8 + - + +
14A ASP* 3.2 9.5 + - - +
16A PHE* 1.3 82.2 - + - +
18A LYS* 1.3 63.6 + - - +
19A TYR 3.2 0.4 - - - -
20A THR* 3.7 17.3 + - - +
24A ASP* 3.0 9.4 + - - -
103A ZN 2.0 37.7 - - - -
86B HIS* 3.6 6.8 + + - -
89B SER* 3.2 30.9 - - - -
90B HIS* 3.4 3.5 + + - -
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Residues in contact with LYS 18 (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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14A ASP* 3.1 25.2 + - - +
15A MET* 2.9 19.2 + - + +
17A HIS* 1.3 80.1 - - - +
19A TYR* 1.3 78.5 + - + +
20A THR 3.6 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