Contacts of the strand formed by residues 93 - 101 (chain A) in PDB entry 1XSC
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 PRO 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A MET* 4.0 18.6 - - + -
7A ALA* 3.0 28.3 - - + +
8A LEU* 2.6 35.6 + - - +
86A ASN* 5.4 4.9 - - + +
87A TYR* 3.2 20.0 - - - +
88A VAL* 3.5 13.9 - - + +
91A ASN 4.7 0.7 - - - +
92A LYS* 1.3 84.7 - - + +
94A LYS* 1.3 55.8 + - - +
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Residues in contact with LYS 94 (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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8A LEU* 3.4 43.3 - - + -
10A ALA* 3.6 24.3 - - + +
47A LYS* 5.5 10.5 - - - +
48A GLY 4.7 3.6 + - - -
49A HIS* 3.4 28.2 + - + +
85A LEU 2.7 22.7 - - - +
86A ASN* 4.4 0.7 - - - -
87A TYR* 2.8 32.8 + - + +
89A ALA* 5.3 7.9 - - + -
92A LYS 3.3 5.4 + - - +
93A PRO* 1.3 72.1 - - - +
95A THR* 1.3 52.3 + - - +
96A VAL* 3.5 12.0 + - + +
154A ATP 5.1 15.1 + - - +
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Residues in contact with THR 95 (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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7A ALA* 4.7 8.1 - - - +
8A LEU 2.7 16.7 + - - -
9A ARG* 4.7 15.9 - - + +
10A ALA 2.6 41.9 + - - +
84A GLU* 3.5 19.7 - - + -
85A LEU 3.3 4.3 - - - -
86A ASN* 2.6 35.4 + - - +
93A PRO 3.9 0.2 + - - -
94A LYS* 1.3 69.6 - - - +
96A VAL* 1.3 53.5 + - - +
97A ILE* 4.5 9.6 - - + -
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Residues in contact with VAL 96 (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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10A ALA* 3.7 13.7 - - + -
11A CYS* 4.4 1.3 - - - +
12A GLY 3.8 11.0 - - - +
47A LYS* 4.2 18.4 - - + -
83A ARG 3.6 0.9 - - - +
84A GLU* 2.8 4.0 - - - -
85A LEU* 2.5 49.5 + - + +
87A TYR* 3.8 22.4 - - + +
94A LYS* 3.9 12.6 - - + +
95A THR* 1.3 75.5 - - - +
97A ILE* 1.3 61.2 + - - +
98A TYR* 3.5 36.6 - - + +
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Residues in contact with ILE 97 (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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9A ARG* 5.8 4.5 - - - +
10A ALA 3.4 9.4 + - - +
11A CYS* 3.5 10.6 - - - +
12A GLY* 2.6 35.2 + - - +
56A ASP* 3.4 20.0 - - - +
82A LYS* 4.0 20.9 - - + -
83A ARG 3.4 6.1 - - - +
84A GLU* 3.2 33.7 - - + +
95A THR* 4.5 7.9 - - + -
96A VAL* 1.3 73.0 - - - +
98A TYR* 1.3 62.4 + - - +
99A TRP* 3.1 42.3 - - + -
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Residues in contact with TYR 98 (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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12A GLY* 3.4 32.5 - - - -
13A LEU 3.8 0.2 - - - -
14A ILE* 3.5 26.0 - - + -
45A PRO* 3.3 22.2 - - + +
47A LYS* 4.5 10.9 - - + +
81A PHE* 3.7 14.4 - - + -
82A LYS* 3.9 1.9 - - - -
83A ARG* 2.7 30.5 + - + +
85A LEU* 3.6 29.2 - - + +
87A TYR* 5.3 1.9 + - - -
96A VAL* 3.5 19.9 - - + +
97A ILE* 1.3 75.7 - - - +
99A TRP* 1.3 66.5 + - - +
136A MET* 2.9 41.8 - - + -
139A ALA* 3.4 18.6 - - + -
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Residues in contact with TRP 99 (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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11A CYS* 3.7 3.4 - - - -
12A GLY 3.6 7.7 + - - -
13A LEU* 2.9 15.8 - - + +
14A ILE* 2.7 30.2 + - - +
56A ASP* 3.2 28.5 - - + -
57A LEU* 3.3 53.6 - - + +
60A ALA* 3.7 11.9 - - + -
77A ILE* 3.6 24.9 - - + -
78A ILE 4.4 6.5 - - - -
79A GLU* 6.1 0.4 - - - -
81A PHE 3.5 18.1 + - - -
82A LYS* 3.2 29.0 - - + +
97A ILE* 3.1 34.3 - - + -
98A TYR* 1.3 73.8 - - - +
100A LEU* 1.3 61.5 + - - +
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Residues in contact with LEU 100 (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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14A ILE* 3.2 16.8 - - + +
16A PHE* 3.6 18.4 - - + -
76A THR 3.2 0.2 - - - +
77A ILE* 3.1 4.4 - - - -
78A ILE* 2.6 49.2 + - + -
81A PHE* 3.0 53.8 - - + -
99A TRP* 1.3 75.7 - - - +
101A ALA* 1.3 57.8 + - - +
143A GLY* 3.5 21.1 - - - +
146A PHE* 3.9 2.7 - - + -
147A LEU* 3.3 33.0 - - + -
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Residues in contact with ALA 101 (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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13A LEU* 3.6 15.7 - - + -
14A ILE 2.8 6.7 + - - -
15A ILE* 3.0 12.1 - - + +
16A PHE* 2.4 42.9 + - - -
75A LEU* 3.8 14.4 - - + -
76A THR 3.1 4.5 - - - -
77A ILE* 3.5 26.9 - - + -
100A LEU* 1.3 74.5 - - - +
102A GLU* 1.3 55.1 + - - +
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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