Contacts of the strand formed by residues 29 - 39 (chain A) in PDB entry 2W27
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 VAL 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ALA* 3.8 9.6 - - + -
21A ILE 3.4 4.9 - - - +
22A PHE* 3.7 27.6 - - + -
28A LYS* 1.3 69.7 - - - +
30A VAL* 1.3 60.1 + - - +
31A GLY 3.7 20.6 - - - +
32A TYR* 3.8 29.8 - - + +
83A LEU* 4.6 3.1 - - + -
241A LEU* 5.2 4.3 - - + -
242A GLU 4.0 9.0 - - - +
243A ARG* 2.8 61.8 + - + +
245A VAL* 5.1 1.8 - - + +
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Residues in contact with VAL 30 (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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21A ILE* 2.8 37.2 + - + +
23A SER* 4.7 9.2 - - - +
28A LYS* 3.2 9.1 + - + +
29A VAL* 1.3 73.9 - - - +
31A GLY* 1.3 59.3 + - - +
82A ASP 4.3 2.2 - - - +
83A LEU* 3.8 8.7 - - - +
84A LEU* 3.0 39.8 + - + +
86A PHE* 4.9 3.4 - - + -
227A TYR* 4.2 28.7 - - + +
243A ARG* 3.8 9.1 + - - +
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Residues in contact with GLY 31 (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 ALA* 3.6 1.0 - - - -
21A ILE* 3.0 26.7 + - - -
29A VAL* 3.5 4.2 - - - +
30A VAL* 1.3 80.9 - - - +
32A TYR* 1.3 70.1 + - - -
83A LEU* 3.6 14.3 - - - +
84A LEU* 3.1 18.8 - - - -
86A PHE* 4.7 1.6 - - - -
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Residues in contact with TYR 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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18A TYR* 3.8 27.1 - - + -
19A GLN 3.2 7.4 - - - +
20A ALA* 3.4 33.9 - - + -
21A ILE* 4.7 0.7 - - - +
29A VAL* 3.8 21.1 - - + +
31A GLY* 1.3 76.4 - - - -
33A GLU* 1.3 61.2 + - - +
34A VAL* 4.0 0.5 + - - +
76A PHE* 4.2 13.1 - + + -
83A LEU* 4.1 12.3 - - + -
84A LEU 3.1 8.5 + - - +
85A ILE* 3.9 1.9 - - - -
86A PHE* 2.9 31.0 + - - +
239A THR 4.9 1.3 - - - -
240A PHE* 3.6 42.5 - + - +
241A LEU* 2.7 46.2 + - + +
243A ARG* 6.0 0.2 - - - +
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Residues in contact with GLU 33 (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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18A TYR* 3.5 5.7 - - - -
19A GLN* 2.8 33.1 + - + +
21A ILE* 4.4 4.8 - - + +
32A TYR* 1.3 72.2 - - - +
34A VAL* 1.3 69.5 + - - +
35A LEU* 3.6 15.9 + - + +
86A PHE* 3.5 13.9 - - + +
88A ASN* 2.7 19.1 - - - +
122A GLU* 3.0 16.0 - - - +
173A LYS* 3.2 5.6 + - - -
209A GLU* 5.8 0.5 - - - -
229A GLN* 2.7 38.5 + - - +
501A 5GP 3.1 11.7 + - - +
503A CA 2.3 30.1 - - - -
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Residues in contact with VAL 34 (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 PRO* 4.1 7.2 - - + -
17A TYR 3.9 3.4 - - - +
18A TYR* 4.4 5.4 - - + -
32A TYR 4.9 0.2 - - - +
33A GLU* 1.3 78.3 - - - +
35A LEU* 1.3 65.0 + - - +
68A ILE* 3.8 28.5 - - + -
69A ILE* 5.5 4.3 - - + +
72A ALA* 3.9 28.0 - - + -
73A LEU* 5.5 0.2 - - + -
76A PHE* 4.2 20.0 - - + -
85A ILE* 4.5 8.5 - - + -
86A PHE 3.0 17.0 + - - +
87A MET* 4.6 9.9 - - + -
88A ASN* 3.9 12.0 + - - +
502A 5GP 4.0 11.5 + - + +
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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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16A PRO* 3.4 7.8 - - - +
17A TYR 3.1 34.6 + - - +
19A GLN* 4.1 17.0 - - + +
33A GLU* 4.2 22.0 - - + +
34A VAL* 1.3 79.3 - - - +
36A GLY* 1.3 59.7 + - - +
37A ARG* 3.5 15.7 - - - +
68A ILE* 4.4 0.3 - - - +
88A ASN* 4.8 0.4 - - - +
236A PRO* 3.8 33.2 - - + -
501A 5GP 3.8 29.2 - - - +
502A 5GP 3.1 36.4 - - + +
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Residues in contact with GLY 36 (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 LEU 4.3 0.4 - - - -
35A LEU* 1.3 71.5 - - - +
37A ARG* 1.3 74.6 + - - +
46A SER* 3.5 0.3 - - - -
47A LEU* 2.8 30.5 + - - -
48A GLY 4.6 0.5 + - - -
68A ILE* 3.8 15.7 - - - -
502A 5GP 2.8 27.3 + - - -
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.4 7.4 - - - +
15A LEU* 2.8 46.6 + - + +
17A TYR* 3.7 35.4 - - + +
35A LEU* 3.5 15.6 - - - +
36A GLY* 1.3 87.7 + - - +
38A ILE* 1.3 61.1 + - - +
44A ILE* 3.9 22.4 - - + +
45A GLN 3.4 14.6 - - - +
46A SER* 3.1 21.5 + - - +
47A LEU* 3.9 5.5 - - - +
236A PRO* 3.9 21.8 - - - +
501A 5GP 3.5 13.9 + - - -
502A 5GP 2.9 28.7 + - - -
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Residues in contact with ILE 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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2A LEU* 3.6 29.6 - - + -
6A ASP 4.6 3.8 - - - +
7A ILE* 3.8 31.2 - - + -
10A ASN* 4.1 12.6 - - + +
13A ASP* 4.0 12.1 - - + +
14A VAL* 3.8 23.1 - - + +
15A LEU* 4.0 4.5 - - - -
37A ARG* 1.3 74.1 - - - +
39A LEU* 1.3 68.1 + - - +
40A ALA* 3.4 9.5 + - + -
44A ILE* 3.5 3.2 - - - -
45A GLN* 3.1 31.8 + - + +
46A SER 5.5 0.2 - - - -
47A LEU* 3.8 15.5 - - + -
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Residues in contact with LEU 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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13A ASP* 3.3 44.8 + - + +
15A LEU* 3.9 7.2 - - + +
38A ILE* 1.3 74.5 - - - +
40A ALA* 1.3 58.4 + - - +
41A ASP 4.2 1.3 + - - +
42A SER* 4.7 6.3 - - - +
43A GLU* 3.3 27.1 - - - +
44A ILE* 3.8 19.5 - - + +
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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