Contacts of the strand formed by residues 25 - 32 (chain B) in PDB entry 4GJC
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 GLN 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B GLY* 3.4 0.3 - - - -
20B ILE 2.8 35.9 + - - +
23B PRO 4.2 5.3 + - - +
24B PRO* 1.3 73.0 - - - +
26B THR* 1.3 60.5 + - - +
27B PHE* 3.3 19.3 - - + -
54B LYS* 5.1 7.0 - - - +
55B LEU 3.8 4.9 - - - +
56B PHE* 3.5 25.1 - - - -
57B ASP* 2.8 49.9 + - - +
60B ASP* 4.1 14.7 + - + +
61B SER* 4.2 8.5 - - - -
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Residues in contact with THR 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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257A ASP* 2.8 29.2 + - - +
268A THR* 3.7 24.2 - - - +
17B GLU* 3.8 20.4 + - + +
18B ILE 3.3 9.9 - - - +
19B GLY* 4.7 6.1 - - - -
24B PRO* 4.7 10.3 - - + +
25B GLN* 1.3 74.3 - - - +
27B PHE* 1.3 62.2 + - - +
54B LYS* 2.7 42.0 + - - +
118B ASP* 4.7 0.2 - - - +
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Residues in contact with PHE 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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16B GLY 3.6 0.2 - - - +
17B GLU* 3.2 9.3 - - - +
18B ILE* 2.9 33.8 + - + +
20B ILE* 4.1 14.4 - - + -
25B GLN* 3.3 35.7 - - + -
26B THR* 1.3 74.0 - - - +
28B LYS* 1.3 63.1 + - - +
29B VAL* 3.7 9.4 + - + -
40B VAL* 3.6 36.1 - - + -
54B LYS* 3.5 40.4 - - + -
55B LEU 3.9 3.1 - - - -
56B PHE* 3.5 45.5 - + + -
118B ASP* 3.6 9.4 - - + +
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Residues in contact with LYS 28 (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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253A PRO 3.5 22.8 + - - -
254A THR 5.4 0.6 - - - -
255A LEU 4.1 11.7 + - - -
257A ASP* 4.2 10.7 + - - -
270A THR* 4.1 30.5 - - + -
271A SER* 4.0 11.4 + - - +
272A ALA 6.1 0.2 - - - +
15B TYR* 3.9 26.1 + - + -
16B GLY 3.3 6.7 - - - +
17B GLU* 4.8 2.5 - - + +
27B PHE* 1.3 70.1 - - - +
29B VAL* 1.3 58.4 + - - +
116B GLU 3.6 16.4 + - - +
117B PHE* 3.9 13.2 - - - -
118B ASP* 2.7 44.7 + - - +
119B GLY 3.1 7.1 + - - -
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Residues in contact with VAL 29 (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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15B TYR* 3.1 7.8 - - - +
16B GLY 2.8 40.6 + - - +
18B ILE* 3.7 44.0 - - + -
27B PHE* 4.1 7.6 - - + -
28B LYS* 1.3 78.6 - - - +
30B VAL* 1.3 59.5 + - - +
31B PHE* 3.8 14.2 - - + -
39B TRP 4.8 0.2 - - - +
40B VAL* 4.3 3.6 - - + -
117B PHE* 4.4 0.9 - - - -
119B GLY* 3.3 24.0 - - - +
120B VAL 4.1 2.2 - - - +
121B VAL* 3.7 26.7 - - + -
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Residues in contact with VAL 30 (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* 5.3 0.2 - - + -
14B TYR 3.4 19.5 - - - +
15B TYR* 4.3 2.0 - - + -
29B VAL* 1.3 73.1 - - - +
31B PHE* 1.3 61.2 + - - +
32B ASP* 3.6 6.8 + - + -
117B PHE* 3.5 38.4 - - + -
119B GLY 3.1 11.1 + - - +
120B VAL* 3.5 5.7 - - + +
121B VAL* 2.8 30.3 + - - +
217B GLY* 4.2 11.4 - - - -
1001B 0MJ 4.4 11.7 - - + -
1002B SO4 3.0 32.1 - - - +
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Residues in contact with PHE 31 (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 VAL* 4.0 32.1 - - + -
6B LEU* 4.0 20.2 - - + -
14B TYR 4.6 3.0 + - - -
16B GLY* 4.1 2.9 - - - -
17B GLU 4.7 0.2 - - - -
18B ILE* 4.0 11.2 - - + -
29B VAL* 3.8 32.3 - - + -
30B VAL* 1.3 71.9 - - - +
32B ASP* 1.3 53.5 + - - +
91B VAL* 4.3 16.4 - - + -
121B VAL* 3.3 37.7 - - + -
123B MET* 4.0 15.9 - - + -
153B PHE* 3.6 24.4 - - + -
155B TYR* 4.1 2.9 + - - -
165B ILE* 4.1 13.0 - - + -
167B LEU* 6.2 0.7 - - + -
216B THR* 2.7 31.3 + - - +
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Residues in contact with ASP 32 (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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30B VAL* 4.2 4.0 - - + -
31B PHE* 1.3 71.2 - - - +
33B THR* 1.3 54.7 + - - +
34B GLY 3.1 5.5 + - - -
35B SER* 2.6 38.2 + - - +
75B TYR* 4.2 0.7 - - - -
120B VAL* 3.9 14.6 - - + -
121B VAL 2.9 8.3 + - - +
123B MET* 2.6 27.7 + - - +
215B ASP* 2.7 14.9 - - - +
216B THR* 3.5 1.3 - - - -
217B GLY* 3.3 10.4 - - - +
1001B 0MJ 2.7 50.3 + - - -
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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