Contacts of the strand formed by residues 88 - 96 (chain N) in PDB entry 5GAH
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 ASN 88 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10N ARG* 4.6 10.4 + - - -
11N LYS* 4.5 8.8 + - - +
74N THR* 3.1 1.3 - - - -
75N GLU 2.9 33.9 + - - +
76N LYS* 5.1 0.2 - - - +
86N LYS 5.2 0.4 - - - +
87N GLY* 1.3 73.9 - - - +
89N VAL* 1.3 66.4 + - - +
90N GLU* 3.2 10.4 + - - +
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Residues in contact with VAL 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N ARG* 3.8 30.7 - - + +
11N LYS* 4.2 20.4 - - + -
72N PRO* 3.9 21.1 - - + -
73N ILE 3.6 12.1 - - - +
74N THR* 4.2 4.0 - - + +
88N ASN* 1.3 74.6 - - - +
90N GLU* 1.3 67.0 + - - +
91N TYR 4.4 7.0 - - - +
92N TRP* 4.6 15.5 - - + +
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Residues in contact with GLU 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N ILE 2.9 13.8 + - - +
74N THR 4.6 0.4 - - - -
75N GLU* 3.3 47.0 - - + +
88N ASN* 3.2 16.5 + - - +
89N VAL* 1.3 78.7 - - - +
91N TYR* 1.3 83.5 + - + +
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Residues in contact with TYR 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40N ARG* 5.7 1.1 + - - -
42N THR* 4.5 16.2 - - + -
44N ARG* 5.9 9.6 - - + +
72N PRO* 3.7 3.8 - - - +
73N ILE* 2.9 52.0 + - + +
75N GLU* 3.4 27.4 + - - -
89N VAL* 3.7 1.9 - - - +
90N GLU* 1.3 104.0 - - + +
92N TRP* 1.3 76.2 + - - +
93N VAL* 3.8 22.0 - - + -
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Residues in contact with TRP 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2N LEU 4.8 5.6 - - - +
3N GLN* 3.0 48.1 + - + -
4N PRO* 3.6 26.5 - - + -
7N THR* 4.4 21.1 - - + -
9N PHE 5.6 0.7 - - - -
10N ARG 5.2 3.6 - - - -
42N THR* 3.3 3.1 - - - -
43N ALA* 3.1 27.8 + - + +
69N PRO* 3.7 15.9 - - + +
70N ASP 3.3 29.8 - - - -
71N LYS 3.7 2.2 - - - -
72N PRO* 3.4 39.5 - - + -
89N VAL* 4.6 12.9 - - + +
90N GLU 5.9 0.2 - - - -
91N TYR* 1.3 84.6 - - - +
93N VAL* 1.3 69.2 + - - +
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Residues in contact with VAL 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40N ARG* 4.1 26.0 - - + +
41N LEU 3.2 9.6 - - - +
42N THR* 3.9 13.9 - - + +
69N PRO* 3.1 11.8 - - - +
70N ASP* 3.1 1.2 + - - +
71N LYS* 3.0 53.1 + - + +
73N ILE* 3.7 32.8 - - + -
91N TYR* 3.8 15.5 - - + -
92N TRP* 1.3 82.5 - - - +
94N ALA* 1.3 61.3 + - - +
95N LEU* 5.2 1.1 - - + +
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Residues in contact with ALA 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40N ARG* 3.6 1.9 - - - -
41N LEU* 2.9 37.7 + - + +
46N ILE* 4.7 4.5 - - + -
67N VAL* 4.7 1.1 - - + -
68N PHE 3.1 36.3 - - - +
69N PRO* 3.6 3.4 - - + -
70N ASP* 4.7 2.0 - - - -
93N VAL* 1.3 74.7 - - - +
95N LEU* 1.3 66.2 + - - +
96N ILE* 3.4 17.2 - - + +
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Residues in contact with LEU 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909A A 5.8 4.3 - - - +
958A U 4.6 1.8 - - - +
14N LYS 5.4 0.2 - - - +
15N GLY* 6.1 0.4 - - - -
16N ARG 3.9 20.9 - - - +
17N ASN* 4.0 21.8 - - + +
39N GLY 4.4 0.2 - - - -
40N ARG* 3.5 36.1 - - + +
70N ASP* 5.3 1.8 + - - -
71N LYS* 4.2 33.3 - - + +
93N VAL* 4.2 1.9 + - + -
94N ALA* 1.3 71.7 - - - +
96N ILE* 1.3 65.2 + - - +
97N GLN* 3.0 25.9 + - - +
100N LYS* 4.5 5.7 - - - +
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Residues in contact with ILE 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N ASN* 3.0 10.1 + - - +
35N ALA* 4.0 12.3 - - + -
37N GLY 4.7 0.7 - - - +
38N ARG* 3.4 3.1 - - - -
39N GLY 2.9 46.7 + - - +
41N LEU* 3.5 29.8 - - + -
67N VAL* 4.0 22.7 - - + -
94N ALA* 3.4 20.0 - - + +
95N LEU* 1.3 84.7 - - - +
97N GLN* 1.3 74.0 + - - +
100N LYS* 4.1 9.0 - - + -
102N LEU* 4.1 9.0 - - + -
126N ILE* 3.9 20.2 - - + -
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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