Contacts of the strand formed by residues 3 - 16 (chain B) in PDB entry 2ZJR
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 GLY 3 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LYS* 1.3 78.5 - - - +
4B ILE* 1.3 61.4 + - - +
49B ILE* 4.2 3.6 - - - +
81B PHE* 3.5 21.3 - - - -
84B PHE* 3.8 13.0 - - - -
90B SER* 3.9 12.5 + - - -
95B ILE* 4.9 4.6 - - - +
96B PHE* 3.9 10.7 - - - -
198B LEU 3.2 14.4 - - - -
199B ARG* 4.0 0.2 - - - -
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Residues in contact with ILE 4 (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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3B GLY* 1.3 72.7 - - - -
5B LEU* 1.3 87.4 + - - +
28B ALA* 3.4 28.7 - - + +
29B GLY 4.2 1.6 - - - +
31B CYS* 4.2 8.3 - - + -
49B ILE* 4.4 2.0 - - - -
81B PHE* 4.2 1.6 - - - -
90B SER* 3.1 37.7 - - - +
91B VAL* 3.3 4.0 - - - -
92B ASN* 3.2 31.0 - - - +
95B ILE* 5.2 2.2 - - + -
96B PHE* 4.1 19.6 - - + -
197B VAL* 3.8 4.5 - - - +
198B LEU* 3.1 33.0 + - + +
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Residues in contact with LEU 5 (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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4B ILE* 1.3 85.2 - - - +
6B GLY* 1.3 59.9 + - - +
28B ALA* 3.2 22.2 - - - -
29B GLY 4.0 1.4 + - - -
31B CYS* 3.4 17.6 - - - -
49B ILE* 3.4 20.6 - - + +
50B GLY 4.3 4.3 - - - -
51B TYR* 3.7 26.5 - - + -
77B ILE* 4.0 19.7 - - + -
79B ARG* 4.0 16.4 - - + -
81B PHE* 3.2 41.7 - - + -
195B LEU* 4.3 9.9 - - + -
196B VAL 3.8 3.1 - - - -
197B VAL* 4.6 8.1 - - + -
198B LEU* 5.3 0.9 - - - -
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Residues in contact with GLY 6 (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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5B LEU* 1.3 78.3 - - - +
7B THR* 1.3 61.2 + - - -
26B VAL* 4.6 1.1 - - - -
27B LEU 3.1 12.6 - - - -
28B ALA* 4.0 2.7 - - - -
51B TYR* 4.0 11.8 - - - -
195B LEU* 3.4 10.5 - - - +
196B VAL* 2.8 48.6 + - - +
198B LEU* 5.5 0.2 - - - -
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Residues in contact with THR 7 (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* 1.3 72.9 - - - -
8B LYS* 1.3 76.1 + - - +
9B ILE* 3.4 4.4 - - + +
26B VAL* 4.0 2.2 - - - -
27B LEU* 2.9 34.5 + - - -
51B TYR* 2.6 27.1 + - - -
193B GLY* 3.5 21.3 - - - +
194B GLY 3.4 3.8 - - - -
3M THR* 2.8 28.7 + - - +
5M ILE* 3.6 18.7 - - + +
7M ILE* 6.1 0.2 - - + -
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Residues in contact with LYS 8 (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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7B THR* 1.3 78.7 - - - +
9B ILE* 1.3 64.5 + - - +
10B GLY* 4.4 2.5 - - - +
11B MET* 5.4 5.8 - - - +
24B THR* 4.1 23.1 + - + -
25B VAL 4.2 2.7 - - - -
26B VAL* 4.4 6.3 - - - -
187B ALA* 6.1 0.2 - - - +
188B ILE* 3.3 19.8 + - + +
189B PRO 4.0 9.2 - - - +
190B GLY 2.7 30.2 + - - +
191B ALA 4.1 9.4 - - - +
192B ASN* 3.2 26.0 - - - +
193B GLY* 3.1 18.7 + - - -
194B GLY 3.0 13.4 + - - +
196B VAL* 3.8 19.8 - - + +
2659X C 3.0 11.7 + - - -
2660X C 2.9 20.6 + - - -
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Residues in contact with ILE 9 (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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7B THR* 3.4 11.4 - - + +
8B LYS* 1.3 83.1 - - - +
10B GLY* 1.3 58.1 + - - +
25B VAL* 2.9 22.1 + - + +
26B VAL 4.4 0.2 - - - -
27B LEU* 3.2 33.0 - - + +
181B LEU* 4.2 7.9 - - + -
192B ASN* 4.0 11.2 - - - +
5M ILE* 6.4 0.2 - - + -
7M ILE* 5.6 2.9 - - + -
9M ARG* 3.8 41.2 + - + +
12M LEU* 3.7 22.4 - - + -
13M LEU* 3.2 31.1 - - + +
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Residues in contact with GLY 10 (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* 4.4 1.6 - - - +
9B ILE* 1.3 80.8 - - - +
11B MET* 1.3 61.7 + - - -
24B THR* 3.4 6.1 - - - +
25B VAL* 2.7 34.0 + - - +
192B ASN* 3.9 17.0 + - - -
13M LEU* 4.1 11.2 - - - -
2661X G 5.7 2.5 - - - -
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Residues in contact with MET 11 (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* 5.4 6.7 - - - +
10B GLY* 1.3 78.0 - - - -
12B THR* 1.3 67.0 + - - +
22B PRO* 4.2 10.8 - - + -
23B VAL 2.9 13.0 - - - +
24B THR* 3.3 20.9 - - + +
25B VAL* 4.6 0.7 - - - +
186B GLY 3.7 19.7 - - - +
187B ALA* 4.3 8.1 - - + -
13M LEU* 4.4 8.1 - - - +
63M ARG* 5.3 0.9 - - - -
2659X C 3.8 17.9 - - - -
2660X C 3.9 9.4 - - - +
2661X G 3.1 72.0 + - + +
2708X U 5.7 0.9 - - - +
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Residues in contact with THR 12 (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* 1.3 80.8 - - - +
13B GLN* 1.3 73.2 + - - +
14B ILE* 4.4 2.7 - - + -
22B PRO* 3.6 4.7 - - - +
23B VAL* 3.2 38.0 + - + +
25B VAL* 4.5 13.2 - - + -
13M LEU* 5.5 3.8 - - + -
16M ILE* 3.9 20.0 - - + +
17M GLU* 2.3 34.8 + - - +
62M SER* 4.0 1.6 + - - -
63M ARG* 4.1 5.1 - - - +
2661X G 3.3 17.3 + - - -
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Residues in contact with GLN 13 (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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12B THR* 1.3 77.6 + - - +
14B ILE* 1.3 74.6 + - - +
15B TRP* 3.7 20.0 - - + -
20B ALA* 4.3 18.8 - - + +
21B ILE 4.2 3.8 - - - +
22B PRO* 4.9 3.1 - - + -
86H GLY* 4.9 11.1 + - - -
20M HIS* 3.9 1.9 - - - +
62M SER* 3.3 47.4 + - - +
63M ARG* 3.8 10.6 - - + +
82M PRO* 4.5 8.5 - - - +
2661X G 3.3 22.9 + - - +
2662X C 4.0 25.8 + - - +
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Residues in contact with ILE 14 (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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12B THR* 4.4 3.4 - - + -
13B GLN* 1.3 87.4 - - - +
15B TRP* 1.3 67.7 + - - +
16B LYS* 4.7 1.1 - - + +
21B ILE* 2.6 52.3 + - + +
23B VAL* 4.1 11.0 - - + -
173B VAL* 4.3 22.4 - - + -
174B GLU* 4.3 7.4 - - - +
176B ARG* 5.9 0.4 - - - +
183B LEU* 3.3 33.4 - - + -
16M ILE* 3.9 13.5 - - + +
20M HIS* 2.9 32.5 - - + +
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Residues in contact with TRP 15 (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* 3.7 28.7 - - + -
14B ILE* 1.3 79.9 - - - +
16B LYS* 1.3 61.2 + - - +
17B ASN 3.6 7.1 + - - +
18B ASP 4.0 4.0 - - - -
19B ARG 3.3 7.0 - - - +
20B ALA* 3.1 31.9 - - + +
85H ASP 2.8 26.1 + - - -
20M HIS* 4.0 45.3 - - + +
62M SER* 4.0 11.7 - - - -
82M PRO* 3.9 11.0 - - + -
84M ALA* 3.3 25.8 - - + -
85M SER* 3.7 9.2 - - - -
86M PRO* 3.0 37.9 - - + +
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Residues in contact with LYS 16 (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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14B ILE* 5.3 0.7 - - + -
15B TRP* 1.3 70.8 - - - +
17B ASN* 1.3 77.2 + - - +
19B ARG* 3.1 30.1 + - - +
21B ILE* 3.0 23.3 - - + +
98B GLU* 5.5 3.4 - - - +
99B GLY* 5.2 5.3 - - - +
171B GLU* 3.1 27.8 + - - +
172B VAL 4.4 3.2 + - - -
173B VAL* 3.8 44.6 + - + +
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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