Contacts of the strand formed by residues 19 - 27 (chain B) in PDB entry 2ZJQ
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 ARG 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B TRP* 3.8 2.7 - - - -
16B LYS* 3.3 26.3 + - - +
17B ASN* 3.6 1.5 - - + -
18B ASP* 1.3 80.6 - - - +
20B ALA* 1.3 65.6 + - - +
21B ILE* 3.1 37.8 - - - +
171B GLU* 4.3 20.2 + - - -
173B VAL* 5.6 0.6 - - - +
185B LYS* 2.9 35.0 - - - +
84H ALA* 3.7 18.4 - - + +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLN* 4.2 17.3 - - - +
14B ILE 3.6 3.6 - - - +
15B TRP* 3.0 41.6 - - + +
19B ARG* 1.3 76.7 + - - +
21B ILE* 1.3 61.6 + - - +
22B PRO* 4.4 3.2 - - - +
84H ALA 3.4 10.5 + - - +
85H ASP 3.5 15.5 - - - +
86H GLY* 4.6 2.5 - - - +
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLN* 4.0 3.5 - - - -
14B ILE* 2.6 37.0 + - + +
16B LYS* 3.6 31.9 - - + +
19B ARG* 3.1 47.8 - - - +
20B ALA* 1.3 76.6 - - - +
22B PRO* 1.3 80.3 - - + +
23B VAL* 3.7 8.8 + - + +
173B VAL* 4.7 9.9 - - + -
185B LYS* 3.2 39.0 - - + +
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Residues in contact with PRO 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B MET* 4.3 9.0 - - + -
12B THR 3.5 7.9 - - - +
13B GLN* 4.9 2.9 - - + -
20B ALA 4.4 3.4 - - - +
21B ILE* 1.3 97.1 - - + +
23B VAL* 1.3 66.0 + - - +
185B LYS* 3.6 3.5 - - - +
186B GLY* 3.6 19.5 + - - +
2661X G 3.6 39.9 - - + +
2708X U 3.6 28.0 - - - +
2709X C 5.3 3.6 - - - +
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B MET* 2.8 28.6 - - - +
12B THR* 3.2 24.3 + - + +
14B ILE* 3.6 35.2 - - + -
21B ILE* 3.8 11.9 - - + +
22B PRO* 1.3 82.2 - - - +
24B THR* 1.3 62.9 + - - +
25B VAL* 3.5 0.7 + - + -
173B VAL* 4.5 18.4 - - + -
183B LEU* 4.6 16.2 - - + -
184B VAL 3.0 15.7 - - - +
185B LYS* 4.4 2.7 - - - +
186B GLY 4.3 1.8 - - - -
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS* 4.3 18.0 - - + -
10B GLY 3.6 5.2 - - - +
11B MET* 3.0 21.4 - - - +
23B VAL* 1.3 71.7 - - - +
25B VAL* 1.3 64.7 + - - +
26B VAL* 3.2 28.2 + - + +
183B LEU* 4.5 0.4 - - - -
184B VAL* 2.6 27.6 + - - +
186B GLY 3.2 16.4 + - - -
187B ALA* 3.7 0.9 - - - -
188B ILE* 3.7 33.6 + - + -
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Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 3.0 42.1 + - + +
10B GLY 2.6 22.9 + - - +
12B THR* 4.6 16.4 - - + -
23B VAL* 4.4 5.2 - - + +
24B THR* 1.3 69.8 - - - +
26B VAL* 1.3 66.8 + - - +
181B LEU* 4.3 7.6 - - + -
182B ILE 3.9 2.2 - - - +
183B LEU* 3.2 20.6 - - + -
13M LEU* 4.3 13.9 - - + -
16M ILE* 3.2 33.4 - - + -
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLY* 4.6 0.4 - - - -
7B THR 3.2 18.6 - - - +
8B LYS* 4.5 2.0 - - - -
9B ILE* 4.6 0.9 - - - -
24B THR* 3.3 21.3 - - + +
25B VAL* 1.3 77.7 - - - +
27B LEU* 1.3 67.4 + - - +
28B ALA* 5.3 0.4 - - - -
181B LEU* 3.6 4.2 - - - +
182B ILE* 2.9 45.5 + - + +
184B VAL* 4.5 6.1 - - + -
188B ILE* 3.5 26.0 - - + -
196B VAL* 3.5 25.8 - - + -
198B LEU* 4.1 12.1 - - + -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLY* 2.9 2.0 - - - -
7B THR* 2.6 43.1 + - - +
9B ILE* 3.6 16.8 - - + -
26B VAL* 1.3 73.8 - - - +
28B ALA* 1.3 57.0 + - - +
29B GLY* 3.4 16.6 - - - +
51B TYR* 2.8 30.1 - - - +
179B GLU 4.6 4.9 - - - +
180B ASN* 3.3 8.1 - - + +
181B LEU* 3.7 12.8 - - + -
5M ILE* 5.4 5.4 - - + -
7M ILE* 4.5 14.8 - - + -
12M LEU* 3.6 28.7 - - + -
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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