Contacts of the strand formed by residues 83 - 91 (chain A) in PDB entry 1X5G
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 GLU 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLU* 3.4 8.0 - - - +
58A LYS* 3.5 45.1 + - + +
82A THR* 1.3 83.0 - - - +
84A TYR* 1.3 75.7 + - - +
104A ALA* 3.9 12.1 - - + +
105A VAL* 3.3 23.1 - - - +
106A ARG* 3.9 34.8 + - + +
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 3.8 17.0 - - + -
55A TYR* 5.9 3.6 - + - -
56A MET* 3.1 11.4 - - - +
57A GLU* 3.4 34.1 + - + +
58A LYS 4.5 0.7 - - - +
78A LEU* 3.9 31.5 - - + +
79A LYS* 3.0 39.0 + - - +
82A THR* 3.3 37.0 - - + +
83A GLU* 1.3 84.1 - - - +
85A SER* 1.3 60.9 + - - +
86A PHE* 3.1 35.4 - + + -
103A VAL 3.2 0.2 - - - +
104A ALA* 4.0 3.4 - - - -
105A VAL 3.0 24.7 + - - -
107A THR* 4.3 0.9 - - + -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A TYR* 3.3 2.2 - - - -
56A MET* 2.7 53.9 + - - +
58A LYS* 4.8 10.8 - - - +
63A GLU* 5.0 4.3 + - - -
84A TYR* 1.3 72.3 - - - +
86A PHE* 1.3 75.4 + - - +
87A ARG* 5.8 0.3 + - - -
102A ASP* 3.3 27.7 + - - +
103A VAL 3.6 5.7 + - - -
104A ALA* 3.9 9.2 + - - +
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Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 5.7 1.6 - - + -
26A ALA* 4.8 3.6 - - + -
34A ILE* 3.6 30.5 - - + -
36A VAL* 4.2 26.7 - - + -
53A LEU* 4.6 4.9 - - + -
54A TYR 3.4 16.2 - - - +
55A TYR* 3.3 22.4 - + + -
75A ILE* 3.4 18.6 - - + -
78A LEU* 4.9 2.9 - - + -
84A TYR* 3.1 40.8 - + + -
85A SER* 1.3 82.2 + - - +
87A ARG* 1.3 64.5 + - - +
88A VAL* 6.1 0.2 - - - -
101A PRO 3.8 0.2 - - - +
102A ASP* 3.5 1.7 - - - -
103A VAL* 2.7 53.6 + - + +
105A VAL* 3.7 19.7 - - + -
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 5.3 2.2 - - - -
53A LEU* 3.9 2.1 - - - +
54A TYR* 3.0 54.6 + - + -
56A MET* 5.5 2.0 - - - +
63A GLU* 2.6 41.5 + - - +
85A SER* 5.8 0.4 + - - -
86A PHE* 1.3 77.5 - - - +
88A VAL* 1.3 63.5 + - - +
89A VAL* 4.8 3.1 - - + -
99A SER* 3.7 24.4 + - - +
100A THR* 3.9 21.0 + - - +
101A PRO 4.8 1.6 - - - -
102A ASP* 4.6 17.6 - - - +
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PRO* 5.9 0.2 - - - +
21A ALA* 4.0 23.6 + - + -
24A LEU* 3.7 21.7 - - + +
36A VAL* 5.2 0.2 - - + -
38A TRP* 3.6 47.3 - - + +
51A TYR* 4.2 14.4 - - + -
52A LYS 3.5 7.2 - - - +
53A LEU* 4.5 7.4 - - + -
87A ARG* 1.3 72.8 - - - +
89A VAL* 1.3 76.2 + - - +
98A VAL 4.9 0.3 - - - +
99A SER* 4.2 0.3 - - - -
100A THR* 2.5 40.2 + - - +
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TYR* 4.1 3.3 - - - -
52A LYS* 3.1 29.6 + - - +
54A TYR* 3.9 25.1 - - + -
87A ARG* 4.7 4.5 - - - +
88A VAL* 1.3 87.7 - - - +
90A ALA* 1.3 69.9 + - - +
91A TYR* 3.5 31.1 + - + +
96A PRO* 4.3 10.3 - - + -
97A GLY 4.3 12.1 - - - +
98A VAL 4.4 3.8 - - - +
99A SER* 3.7 23.3 - - - +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PRO* 3.1 46.1 - - + +
19A GLY 4.3 11.8 + - - +
41A PRO* 5.3 2.0 - - + -
48A ILE* 3.6 21.8 - - + -
51A TYR* 4.9 7.6 - - + -
89A VAL* 1.3 73.4 - - - +
91A TYR* 1.3 61.5 + - - +
96A PRO* 3.5 16.5 - - - +
97A GLY 3.6 1.0 + - - -
98A VAL 4.9 4.0 + - - +
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ILE* 3.9 3.3 - - - +
49A GLN* 3.4 28.7 + - + +
50A ASN* 3.7 18.0 + - + +
52A LYS* 3.5 49.9 - - + -
54A TYR* 2.8 21.4 + - - -
89A VAL* 3.5 19.3 - - + +
90A ALA* 1.3 73.0 - - - +
92A ASN* 1.3 60.3 + - - +
95A GLY* 4.7 1.1 - - - -
96A PRO* 3.4 36.9 - - + +
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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