Contacts of the strand formed by residues 9 - 18 (chain A) in PDB entry 3ARE
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 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ASN* 4.1 5.6 + - - +
8A TYR* 1.3 72.5 - - - +
10A PHE* 1.3 65.5 + - - +
11A ARG* 3.5 39.9 + - - +
31A TRP 3.9 2.1 - - - +
32A LEU* 4.9 0.4 - - - -
33A GLY* 3.1 30.6 + - - +
104A CYS 4.3 1.6 - - - -
105A GLU* 3.5 37.7 + - + +
115A PHE* 4.7 4.5 - - + -
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Residues in contact with PHE 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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8A TYR 4.0 1.0 + - - -
9A THR* 1.3 72.9 - - - +
11A ARG* 1.3 62.8 + - - +
12A CYS* 3.7 22.7 - - - -
30A VAL* 3.6 31.9 - - + -
31A TRP 3.4 10.8 - - - -
32A LEU* 3.8 25.8 - - + -
37A THR* 4.4 2.9 - - - -
103A GLY* 3.5 5.0 - - - -
104A CYS 3.2 35.5 + - - +
115A PHE* 3.8 5.0 - - - -
168A CYS* 4.1 8.3 - - - -
171A PHE* 4.0 17.5 - + - -
172A VAL* 3.5 30.1 - - + -
175A LEU* 3.7 20.9 - - + -
601A 4GH 4.2 16.6 - - + -
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Residues in contact with ARG 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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9A THR* 3.5 36.6 - - - +
10A PHE* 1.3 76.2 - - - +
12A CYS* 1.3 62.3 + - - +
13A LEU* 4.0 19.6 + - + +
29A VAL 4.1 0.3 - - - +
30A VAL* 3.5 3.6 - - - +
31A TRP* 2.9 58.9 + - + +
33A GLY 5.2 3.8 - - - -
101A SER* 4.5 11.5 + - - +
102A ALA 3.5 6.1 - - - +
115A PHE* 4.3 18.3 - - + -
58B LYS* 5.8 7.7 - - - +
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Residues in contact with CYS 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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10A PHE* 3.7 26.9 - - - -
11A ARG* 1.3 70.5 - - - +
13A LEU* 1.3 61.9 + - - +
14A GLN 3.9 0.3 + - - -
29A VAL 3.8 3.6 - - - -
30A VAL* 3.7 17.9 - - - -
100A LEU 3.4 6.6 - - - +
101A SER* 3.5 0.9 - - - -
102A ALA* 2.6 39.4 + - + +
601A 4GH 3.9 57.3 - - + +
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Residues in contact with LEU 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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11A ARG* 4.2 18.8 - - + +
12A CYS* 1.3 76.1 - - - +
14A GLN* 1.3 60.9 + - - +
15A MET* 4.1 0.7 + - - +
27A ASP 4.0 0.7 - - - +
28A SER* 3.2 6.5 - - - -
29A VAL* 2.8 51.8 + - + +
30A VAL* 4.8 0.2 - - - +
31A TRP* 3.9 18.2 - - + +
100A LEU 3.3 1.3 - - - -
101A SER* 3.4 26.9 - - - +
601A 4GH 5.3 1.3 - - - +
55B SER* 3.3 26.2 - - - +
56B PHE* 3.6 44.2 - - + +
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Residues in contact with GLN 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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12A CYS 3.9 0.6 + - - -
13A LEU* 1.3 73.2 - - - +
15A MET* 1.3 65.4 + - - +
16A SER* 3.1 19.9 + - - +
26A THR* 3.9 21.3 - - + +
27A ASP 3.9 2.7 - - - -
28A SER* 4.0 10.3 - - - +
73A TYR* 2.7 39.5 + - - -
77A PHE* 3.4 23.3 - - - -
98A ILE* 4.6 1.8 - - - +
99A GLN* 3.3 6.1 - - - -
100A LEU* 2.8 57.9 + - + +
601A 4GH 4.0 11.5 - - + +
56B PHE* 3.8 1.9 - - - -
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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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13A LEU 4.9 0.7 - - - +
14A GLN* 1.3 76.4 - - - +
16A SER* 1.3 61.4 + - - +
17A SER* 5.1 2.8 + - - +
25A ARG* 3.7 2.3 - - - +
26A THR* 3.4 2.1 - - - -
27A ASP* 2.9 59.1 + - + +
29A VAL* 4.6 8.5 - - - -
98A ILE 3.9 2.9 - - - -
99A GLN* 4.8 1.3 - - + +
33B PRO* 4.9 7.4 - - + -
54B MET* 3.3 55.2 - - + +
55B SER* 4.3 2.2 - - - -
56B PHE* 3.7 22.0 - - + -
62B PHE* 3.6 28.0 - - + -
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Residues in contact with SER 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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14A GLN* 3.1 21.3 + - - -
15A MET* 1.3 72.3 - - - +
17A SER* 1.3 61.6 + - - +
18A PHE* 4.2 12.9 - - - -
25A ARG 3.4 3.8 - - - -
26A THR* 2.7 26.3 + - - +
77A PHE* 3.7 20.0 - - - -
96A ILE 4.1 0.5 - - - +
97A GLU* 3.5 4.1 + - - +
98A ILE* 2.8 45.7 + - - +
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Residues in contact with SER 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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15A MET 4.1 2.5 + - - -
16A SER* 1.3 73.9 - - - +
18A PHE* 1.3 65.5 + - - +
19A ALA 4.1 0.4 - - - -
23A TRP* 4.5 9.4 - - - -
24A SER* 3.2 7.4 - - - -
25A ARG* 3.0 46.3 + - - +
96A ILE 3.7 0.7 - - - -
97A GLU* 2.6 31.7 + - - -
33B PRO* 3.5 14.7 - - - +
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Residues in contact with PHE 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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16A SER* 4.2 18.4 - - - -
17A SER* 1.3 74.3 - - - +
19A ALA* 1.3 60.4 + - - +
23A TRP 3.7 3.4 - - - +
24A SER* 3.5 26.9 - - - -
26A THR* 5.6 1.1 - - - -
77A PHE* 4.6 5.2 - + - -
78A THR* 3.7 31.9 - - + -
81A ILE* 3.6 32.3 - - + -
82A GLN* 4.0 19.3 - - + -
94A TYR* 3.6 22.2 - + + -
95A PRO* 3.1 7.3 - - - +
96A ILE* 2.7 52.6 + - + +
97A GLU* 4.5 1.3 + - - -
98A ILE* 3.7 19.7 - - + -
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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