Contacts of the helix formed by residues 6 - 17 (chain D) in PDB entry 2W93
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 LEU 6 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D ILE 3.6 1.2 + - - -
5D THR* 1.3 70.4 - - - +
7D GLY* 1.3 63.1 + - - +
9D TYR* 3.1 10.3 - - + +
10D LEU* 3.0 22.7 + - - +
139D ILE* 4.5 1.8 - - + -
142D ILE* 4.2 8.7 - - + -
145D ALA* 3.4 34.5 - - + -
146D PRO* 4.1 7.6 - - + -
149D ILE* 3.6 23.1 - - + +
167D LEU* 4.2 23.1 - - + -
171D LEU* 3.4 38.1 - - + +
172D VAL* 3.5 2.7 + - + +
174D LEU 3.0 12.5 + - - +
176D VAL* 4.0 16.5 - - + +
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Residues in contact with GLY 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 1.3 74.7 - - - +
8D LYS* 1.3 61.8 + - - +
10D LEU* 3.2 13.7 + - - +
11D PHE* 3.3 18.4 - - - -
33D LEU* 3.7 24.0 - - - -
36D LYS* 3.7 13.0 - - - -
167D LEU* 6.0 0.9 - - - -
172D VAL* 2.9 21.8 + - - +
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Residues in contact with LYS 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 3.7 22.9 - - + -
5D THR* 3.1 22.2 + - - +
7D GLY* 1.3 76.0 - - - +
9D TYR* 1.3 58.4 + - - +
11D PHE* 3.2 3.9 + - - +
12D GLU* 2.9 56.3 + - + +
36D LYS* 3.6 15.4 - - + +
39D GLU* 3.4 43.8 + - - +
40D VAL* 3.7 12.1 - - + -
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Residues in contact with TYR 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 4.1 9.9 - - + +
5D THR 2.8 13.2 + - - +
6D LEU* 3.1 14.8 - - + +
8D LYS* 1.3 75.4 - - - +
10D LEU* 1.3 65.0 + - - +
12D GLU* 3.2 5.6 + - - +
13D ARG* 3.0 39.4 + - + +
146D PRO* 3.4 35.4 + - + +
149D ILE* 4.0 19.1 - - + -
150D ASP* 2.8 38.8 + - - -
176D VAL* 3.8 20.2 - - + -
177D PRO 4.8 1.3 - - - -
180D LEU* 4.0 18.2 - - + +
181D LEU* 3.7 28.4 - - + +
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Residues in contact with LEU 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU 3.0 11.5 + - - +
7D GLY* 3.4 9.9 - - - +
9D TYR* 1.3 82.2 - - - +
11D PHE* 1.3 70.3 + - + +
13D ARG* 3.2 3.3 + - - +
14D LEU* 3.0 45.2 + - + +
33D LEU* 4.2 13.2 - - + -
71D ILE* 4.8 1.8 - - + -
96D LEU* 4.5 6.1 - - + -
98D VAL* 4.2 17.7 - - + -
149D ILE* 3.9 29.2 - - + -
153D ILE* 4.4 6.1 - - + -
165D LEU* 4.4 13.0 - - + -
167D LEU* 4.1 24.0 - - + -
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Residues in contact with PHE 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D GLY 3.3 22.6 + - - -
8D LYS* 3.2 3.6 + - - +
10D LEU* 1.3 76.9 - - + +
12D GLU* 1.3 66.5 + - - +
14D LEU* 3.8 21.4 - - + +
15D LYS* 3.0 24.8 + - - +
22D VAL* 4.1 7.2 - - + -
33D LEU* 3.2 37.0 - - + -
34D LEU* 4.9 0.2 - - + -
36D LYS* 3.8 5.2 - - + +
37D ILE* 3.3 45.5 - - + -
40D VAL* 3.8 22.5 - - + +
43D MET* 4.1 16.9 - - + +
71D ILE* 3.5 31.6 - - + -
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Residues in contact with GLU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 4.1 8.4 - - + +
8D LYS* 2.9 42.9 + - + +
9D TYR 3.2 5.1 + - - +
11D PHE* 1.3 79.0 - - - +
13D ARG* 1.3 60.3 + - - +
15D LYS* 3.5 13.7 + - - +
16D GLN* 3.1 33.9 + - - +
39D GLU 5.0 0.2 - - - +
40D VAL* 3.9 22.5 - - + +
181D LEU* 3.8 28.5 - - + -
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Residues in contact with ARG 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D TYR* 3.0 33.7 + - + +
10D LEU* 3.5 9.0 - - - +
12D GLU* 1.3 72.7 - - - +
14D LEU* 1.3 67.4 + - - +
16D GLN* 2.9 35.3 + - - +
17D VAL* 3.2 19.8 + - - +
149D ILE* 4.7 0.4 - - + -
150D ASP* 2.9 42.1 + - - +
153D ILE* 3.6 19.3 - - + -
180D LEU* 3.3 13.5 + - - +
181D LEU* 3.5 25.4 + - + +
183D THR 2.9 31.1 + - - -
184D PRO* 3.8 2.8 - - - +
185D ILE* 3.4 22.0 - - + +
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 3.0 29.4 + - + +
11D PHE* 3.8 30.5 - - + +
13D ARG* 1.3 76.1 - - - +
15D LYS* 1.3 62.2 + - - +
17D VAL* 3.0 14.8 + - + +
19D VAL* 3.0 51.1 + - + +
22D VAL* 4.4 6.3 - - + -
43D MET* 4.2 2.7 - - + -
67D MET* 4.6 4.0 - - + -
69D CYS* 3.8 36.1 - - + -
96D LEU* 4.3 10.3 - - + -
153D ILE* 4.2 17.3 - - + -
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Residues in contact with LYS 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE 3.0 17.2 + - - +
12D GLU* 3.6 13.0 + - - +
14D LEU* 1.3 75.2 - - - +
16D GLN* 1.3 62.4 + - + +
18D ASN* 3.1 16.6 + - - +
19D VAL 3.7 9.1 + - - -
20D ASN* 4.0 16.7 + - - +
40D VAL* 3.7 13.9 - - + +
41D GLU* 3.1 45.1 + - - +
42D GLY* 5.4 2.2 - - - -
43D MET* 3.8 9.4 - - + -
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Residues in contact with GLN 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLU* 3.1 18.3 + - - +
13D ARG* 2.9 40.6 + - - +
15D LYS* 1.3 78.8 - - + +
17D VAL* 1.3 63.4 + - + +
18D ASN* 3.4 7.4 + - - +
181D LEU* 3.0 35.1 + - - +
184D PRO* 4.4 9.5 - - - +
185D ILE* 4.8 1.4 + - - +
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Residues in contact with VAL 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG 3.2 13.4 + - - +
14D LEU* 3.0 23.1 + - + +
16D GLN* 1.3 83.5 - - + +
18D ASN* 1.3 72.7 + - - +
19D VAL* 3.4 9.9 + - + +
65D LYS 5.4 1.2 - - - +
67D MET* 4.0 26.0 + - - +
153D ILE* 4.1 13.2 - - + -
185D ILE* 4.6 8.3 - - + -
187D MET* 3.8 39.3 - - + -
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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