Contacts of the strand formed by residues 50 - 56 (chain B) in PDB entry 5GT8
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 ASP 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B SER* 3.4 30.8 - - - -
15B VAL 3.6 11.4 - - - +
16B ALA* 4.3 11.0 + - - +
17B ARG 4.8 0.7 - - - +
45B THR 4.0 0.3 - - - +
47B THR* 2.7 38.9 + - - +
49B GLU* 1.3 98.1 - - + +
51B TYR* 1.3 69.2 + - - +
52B THR* 3.9 5.4 - - - +
70B GLN* 5.5 1.9 - - - +
301B PHE* 5.4 2.2 - - + -
302B ASN* 4.4 15.1 + - - +
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Residues in contact with TYR 51 (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 LEU 3.8 0.2 - - - +
14B SER* 3.6 1.2 - - - -
15B VAL* 2.9 50.6 + - + +
17B ARG* 2.6 55.5 + - + -
20B LEU* 3.6 52.6 - - + +
44B LEU* 4.0 20.0 - - + -
45B THR 3.4 4.7 - - - +
46B GLU* 3.4 39.9 + - + -
50B ASP* 1.3 74.6 - - - +
52B THR* 1.3 62.2 + - - +
53B LEU* 3.7 3.7 + - + +
205B LEU* 3.2 21.8 + - + -
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Residues in contact with THR 52 (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 VAL* 4.3 8.7 - - + -
13B LEU 3.3 12.1 - - - +
14B SER* 4.6 0.7 - - - +
43B SER 3.9 0.7 - - - +
44B LEU* 3.5 1.0 - - - -
45B THR* 2.9 42.0 + - - -
47B THR* 5.2 1.7 + - - -
50B ASP* 3.9 6.3 + - - +
51B TYR* 1.3 73.0 - - - +
53B LEU* 1.3 72.5 + - - +
54B MET* 4.7 7.6 - - + -
299B SER 4.8 2.7 - - - +
300B THR* 3.4 21.1 - - - -
301B PHE* 3.0 40.7 + - + +
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Residues in contact with LEU 53 (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 ARG 4.2 0.9 - - - -
12B VAL* 3.3 3.1 - - - +
13B LEU* 2.9 42.9 + - + +
15B VAL* 4.2 19.5 - - + -
23B TYR* 6.1 0.2 - - + -
27B LEU* 3.8 28.5 - - + -
42B PHE* 5.0 0.4 - - + -
43B SER 3.2 4.9 - - - +
44B LEU* 3.2 42.4 - - + -
51B TYR* 4.1 10.8 - - + +
52B THR* 1.3 80.2 - - - +
54B MET* 1.3 70.9 + - - +
55B VAL* 4.2 10.8 - - + -
63B LEU* 4.3 22.4 - - + -
69B LEU* 5.7 0.2 - - + -
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Residues in contact with MET 54 (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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10B VAL* 3.8 14.1 - - + -
11B ARG 3.2 4.9 - - - -
12B VAL* 4.0 19.5 - - + -
41B PHE* 3.4 15.5 - - + -
42B PHE* 3.4 0.3 - - - -
43B SER* 2.9 42.3 + - - +
45B THR* 5.9 0.7 - - - +
52B THR* 4.7 8.1 - - + -
53B LEU* 1.3 80.3 - - - +
55B VAL* 1.3 60.8 + - - +
113B LEU* 4.3 12.8 - - + -
114B MET 5.5 1.3 - - - +
115B LEU* 3.7 48.5 - - + +
124B LEU* 4.0 21.8 - - + -
299B SER* 4.4 15.5 - - - +
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Residues in contact with VAL 55 (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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10B VAL* 3.7 3.7 - - - +
11B ARG* 2.8 36.8 + - - +
13B LEU* 4.2 14.1 - - + -
30B LEU* 4.7 8.7 - - + -
39B CYS* 5.2 1.3 - - - -
41B PHE 3.2 5.4 - - - +
42B PHE* 3.6 31.4 - - + -
53B LEU* 4.5 7.6 - - + -
54B MET* 1.3 84.1 - - - +
56B ASP* 1.3 68.0 + - - +
59B GLY* 4.4 7.2 - - - -
60B PHE* 3.9 27.8 - - + +
63B LEU* 4.2 9.2 - - + -
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Residues in contact with ASP 56 (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 HIS* 4.5 5.3 + - + +
9B ARG 3.2 24.0 - - - +
10B VAL* 4.2 0.7 - - - +
38B ARG 4.7 0.2 - - - +
39B CYS* 3.4 13.6 - - - +
40B LYS* 2.5 36.8 + - - +
41B PHE* 3.0 26.2 + - + +
55B VAL* 1.3 75.3 - - - +
57B GLU* 1.3 64.7 + - - +
58B GLU* 3.4 6.6 + - - -
59B GLY 2.8 23.0 + - - -
60B PHE 2.9 9.0 + - - -
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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