Contacts of the strand formed by residues 14 - 24 (chain A) in PDB entry 4WNP
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 PHE 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 3.4 4.9 - - - -
11A VAL* 2.9 36.5 + - + +
12A GLY 3.1 0.2 - - - -
13A LYS* 1.3 93.0 - - + +
15A GLU* 1.3 61.6 + - - +
16A PHE* 5.7 1.1 - - + -
34A ARG 3.4 4.5 - - - +
35A HIS* 3.7 37.9 - + + -
36A ARG* 3.6 6.0 - - - -
41A LEU* 4.6 5.6 - - + -
43A VAL* 3.4 36.1 - - + -
45A VAL* 5.6 2.5 - - + -
79A TYR* 4.2 17.3 - + + -
80A ASP* 4.3 20.0 - - + -
91A VAL* 3.7 31.2 - - + -
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Residues in contact with GLU 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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8A THR* 3.7 21.9 - - + +
9A GLU 3.2 12.3 - - - +
10A THR* 4.3 4.5 - - + +
14A PHE* 1.3 77.5 - - - +
16A PHE* 1.3 64.8 + - - +
33A GLY* 3.1 3.6 - - - -
34A ARG* 2.7 83.9 + - + +
36A ARG* 3.5 27.4 + - + +
39A HIS* 3.8 7.3 - - - -
43A VAL* 4.8 0.9 - - - +
45A VAL* 5.4 0.2 - - - -
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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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8A THR* 3.7 3.5 - - - -
9A GLU* 2.8 61.2 + - + +
11A VAL* 4.0 21.1 - - + -
14A PHE 5.6 0.7 - - - -
15A GLU* 1.3 80.4 - - - +
17A SER* 1.3 64.7 + - - +
18A ARG* 4.0 17.3 - - + -
31A PHE* 3.6 37.2 - + + -
32A LYS 3.6 17.0 - - - +
33A GLY* 3.8 7.4 - - - -
45A VAL* 3.7 31.6 - - + -
47A CYS* 4.2 4.5 - - - -
89A TYR* 4.0 20.4 - + - -
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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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7A GLY 3.8 19.5 - - - -
8A THR* 4.8 4.3 - - - -
9A GLU* 5.7 0.2 - - - -
16A PHE* 1.3 78.6 - - - +
18A ARG* 1.3 59.1 + - - +
19A LYS* 3.0 23.9 - - - +
20A ASP* 2.9 45.5 + - - +
31A PHE* 4.1 8.3 - - - +
32A LYS 4.3 0.6 + - - +
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Residues in contact with ARG 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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7A GLY 4.7 2.8 + - - -
9A GLU* 2.5 42.4 + - - +
16A PHE* 4.0 8.9 - - + -
17A SER* 1.3 69.7 - - - +
19A LYS* 1.3 62.6 + - - +
20A ASP 3.2 0.7 - - - -
21A LEU* 4.1 4.9 + - - +
29A VAL* 5.9 1.0 - - - +
31A PHE* 3.4 55.7 - - + -
47A CYS* 4.5 8.1 - - - +
48A ILE 5.6 2.4 + - - -
89A TYR* 3.3 28.3 + - - -
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Residues in contact with LYS 19 (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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17A SER* 3.0 26.1 - - - +
18A ARG* 1.3 80.1 - - - +
20A ASP* 1.3 88.6 + - - +
21A LEU* 3.2 6.6 + - - +
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Residues in contact with ASP 20 (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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17A SER* 2.9 27.6 + - - +
19A LYS* 1.3 109.0 + - - +
21A LEU* 1.3 59.0 + - - +
22A ILE* 3.4 0.4 + - - -
31A PHE* 3.3 7.1 - - - -
32A LYS* 2.9 48.4 + - + +
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Residues in contact with LEU 21 (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 ARG 4.1 4.6 + - - +
19A LYS 3.2 7.4 + - - +
20A ASP* 1.3 72.5 - - - +
22A ILE* 1.3 61.2 + - - +
23A GLY* 3.5 13.5 - - - +
24A HIS* 4.9 15.0 - - + +
29A VAL* 3.4 32.8 - - + -
30A VAL 3.5 12.8 - - - +
31A PHE* 3.8 13.2 - - + -
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Residues in contact with ILE 22 (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 ASP 3.4 0.6 + - - +
21A LEU* 1.3 76.1 - - - +
23A GLY* 1.3 55.8 + - - +
30A VAL* 2.7 16.8 + - + +
31A PHE 3.9 3.6 - - - -
32A LYS* 3.6 43.3 - - + +
44A ALA* 4.0 17.9 - - + -
94A TYR* 3.8 21.5 - - + -
303A 3RJ 3.4 54.4 + - + +
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Residues in contact with GLY 23 (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 LEU* 3.5 12.6 - - - +
22A ILE* 1.3 83.8 - - - +
24A HIS* 1.3 60.1 + - - -
29A VAL* 3.6 1.0 - - - -
30A VAL* 2.8 41.5 + - - +
303A 3RJ 4.5 12.1 - - - -
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Residues in contact with HIS 24 (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 LEU* 4.9 14.4 - - + +
23A GLY* 1.3 75.2 - - - +
25A GLY* 1.3 64.7 + - - +
28A ALA 3.8 2.5 - - - -
29A VAL* 4.2 20.7 - - + +
49A ASN* 3.7 25.2 + - - -
51A LYS* 6.2 2.2 - - + +
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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