Contacts of the strand formed by residues 97 - 107 (chain A) in PDB entry 3I8C
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 SER 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A GLN* 3.0 7.1 - - - +
94A SER* 2.5 46.7 + - - -
96A GLU* 1.3 97.9 + - - +
98A ILE* 1.3 70.2 + - - +
99A ASP* 4.8 4.9 - - - -
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Residues in contact with ILE 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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52A VAL* 5.0 7.9 - - + +
53A LYS* 3.6 38.2 + - + +
91A TYR* 3.1 31.9 - - + +
92A LYS 3.6 2.7 - - - -
93A GLN* 4.0 17.5 - - + +
96A GLU 3.9 7.0 - - - +
97A SER* 1.3 93.3 - - - +
99A ASP* 1.3 70.0 + - - +
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Residues in contact with ASP 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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53A LYS* 5.2 1.8 - - - +
91A TYR* 4.5 2.3 - - - -
92A LYS* 2.9 48.5 + - + +
94A SER* 4.3 13.5 + - - -
97A SER* 4.8 4.9 - - - -
98A ILE* 1.3 84.2 + - - +
100A ILE* 1.3 68.5 + - - +
101A ILE* 5.0 5.4 - - + +
1063A LYS* 6.0 1.7 - - - -
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Residues in contact with ILE 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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23A PHE* 4.6 6.7 - - + -
39A LEU* 5.8 3.1 - - + -
41A ILE* 4.0 17.5 - - + -
53A LYS* 3.5 33.3 - - + +
55A VAL* 4.1 24.2 - - + -
89A LEU* 3.8 42.4 - - + -
90A GLU 3.5 5.6 - - - +
91A TYR* 4.3 15.7 - - + -
99A ASP* 1.3 78.4 - - - +
101A ILE* 1.3 62.0 + - - +
102A THR* 4.2 1.2 + - - -
1065A VAL* 4.4 16.8 - - + +
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Residues in contact with ILE 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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89A LEU* 3.3 9.2 - - - -
90A GLU* 2.9 61.4 + - + +
92A LYS* 4.7 24.9 - - + +
99A ASP* 3.8 8.4 + - + +
100A ILE* 1.3 75.6 - - - +
102A THR* 1.3 66.6 + - - +
103A ARG* 3.5 12.1 + - + -
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Residues in contact with THR 102 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A CYS* 4.4 1.3 - - + -
88A ILE 3.5 6.3 - - - +
89A LEU* 4.3 0.9 - - + -
100A ILE 5.0 1.2 + - - -
101A ILE* 1.3 80.3 - - - +
103A ARG* 1.3 61.0 + - - +
104A ALA* 3.3 26.6 + - - +
105A HIS* 4.4 1.1 - - - +
1064A SER 5.0 0.5 + - - -
1065A VAL* 2.3 39.3 + - - +
1066A GLY* 3.8 19.2 - - - +
1067A LYS* 3.9 32.4 + - + +
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Residues in contact with ARG 103 (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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72A GLU* 2.6 35.6 + - - -
76A LEU* 4.3 16.6 - - + +
88A ILE* 3.0 27.2 + - + +
90A GLU* 3.0 43.2 + - + +
101A ILE* 3.5 8.2 + - + +
102A THR* 1.3 72.3 - - - +
104A ALA* 1.3 63.2 + - + +
147A ARG* 5.9 4.3 - - - +
150A LYS* 4.0 27.5 - - - +
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A ILE* 2.9 37.3 + - + -
102A THR* 3.3 9.4 - - - +
103A ARG* 1.3 82.6 - - + +
105A HIS* 1.3 70.8 + - - +
148A ASP 5.3 1.6 - - - +
149A ASN 4.4 1.1 - - - +
150A LYS* 3.4 24.9 - - + +
152A LEU* 4.0 19.1 - - + -
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Residues in contact with HIS 105 (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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86A ALA 3.4 13.5 - - - +
87A CYS* 4.0 1.6 - - + -
102A THR* 4.0 2.4 + - + +
104A ALA* 1.3 81.0 - - - +
106A GLY* 1.3 63.3 + - - +
150A LYS 3.1 12.0 + - - -
151A GLU* 3.1 27.1 - - + +
152A LEU* 3.4 11.5 - - - +
1066A GLY 3.1 29.2 - - - +
1067A LYS* 3.2 35.7 + - + +
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Residues in contact with GLY 106 (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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85A ASN* 3.9 1.9 - - - -
86A ALA* 2.7 39.6 + - - +
105A HIS* 1.3 83.4 - - - +
107A ASN* 1.3 55.2 + - - -
108A VAL* 4.7 2.9 - - - -
151A GLU* 4.1 11.4 - - - -
152A LEU* 3.9 6.2 - - - +
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Residues in contact with ASN 107 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A LYS 3.1 23.2 + - - -
84A TYR 3.2 10.1 - - - -
85A ASN* 3.8 9.7 - - - +
106A GLY* 1.3 72.8 - - - -
108A VAL* 1.3 60.8 + - - +
109A GLN* 2.7 40.5 + - - +
1072A PHE* 3.4 25.3 - - - -
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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