Contacts of the strand formed by residues 98 - 105 (chain A) in PDB entry 7KHI
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 VAL 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A VAL* 3.3 36.8 - - + -
95A LYS* 3.7 18.8 - - + +
97A GLU* 1.3 77.8 - - - +
99A ILE* 1.3 69.5 + - - +
100A LEU* 3.5 19.1 - - + -
118A ASP* 4.3 9.2 - - + +
121A VAL* 3.7 17.3 - - + -
144A ILE 3.6 0.3 - - - +
145A LYS* 3.3 3.8 - - - +
146A VAL* 2.9 46.4 + - + +
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Residues in contact with ILE 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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97A GLU* 4.4 11.4 - - + +
98A VAL* 1.3 81.4 - - - +
100A LEU* 1.3 62.1 + - - +
101A THR* 4.0 10.8 + - + +
118A ASP* 4.3 8.1 - - - +
143A ARG* 4.0 31.9 - - + -
144A ILE 3.5 7.4 - - - +
145A LYS* 4.0 22.7 - - + +
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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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88A LEU* 5.4 4.3 - - + -
90A VAL* 4.8 2.5 - - + -
98A VAL* 3.5 25.8 - - + -
99A ILE* 1.3 73.8 - - - +
101A THR* 1.3 60.8 + - - +
102A LEU 4.2 0.6 + - - -
115A ILE* 3.6 32.8 - - + -
116A THR* 5.1 4.3 - - - +
118A ASP* 4.6 10.5 - - - +
121A VAL* 4.0 25.1 - - + -
123A ILE* 4.1 16.6 - - + -
143A ARG* 3.2 5.0 - - - -
144A ILE* 2.8 44.8 + - + +
146A VAL* 3.8 22.4 - - + -
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Residues in contact with THR 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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99A ILE* 4.1 12.8 - - + +
100A LEU* 1.3 78.5 - - - +
102A LEU* 1.3 61.0 + - - +
103A ASN* 4.0 15.1 + - - -
115A ILE* 4.2 3.1 - - - -
116A THR* 3.0 44.5 + - + +
142A MET 3.4 7.4 - - - -
143A ARG* 4.6 15.5 - - + -
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Residues in contact with LEU 102 (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 LEU* 6.1 0.2 - - + -
100A LEU 4.2 0.8 - - - -
101A THR* 1.3 70.4 - - - +
103A ASN* 1.3 77.4 + - - +
104A LYS 5.0 1.1 - - - +
110A VAL* 3.7 24.0 - - + -
111A THR 4.5 4.0 - - - +
114A ASP* 3.2 47.6 - - + +
115A ILE* 3.4 22.7 - - + +
130A ILE* 4.8 9.4 - - + -
140A ILE* 3.7 4.1 - - + +
141A SER* 3.3 2.6 - - - -
142A MET* 2.9 62.2 + - + +
144A ILE* 4.8 5.7 - - + +
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Residues in contact with ASN 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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101A THR* 4.0 14.7 + - - -
102A LEU* 1.3 96.4 + - - +
104A LYS* 1.3 62.1 + - - +
114A ASP 5.0 3.2 + - - +
140A ILE 3.4 4.9 - - - +
141A SER* 2.8 26.4 - - - -
142A MET 3.6 3.1 + - - +
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Residues in contact with LYS 104 (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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102A LEU* 4.2 2.5 - - + +
103A ASN* 1.3 75.9 - - - +
105A SER* 1.3 78.2 + - - +
106A GLY 4.2 6.7 + - - -
107A ILE 4.9 1.6 + - - -
108A GLY* 4.2 23.2 + - - -
109A PRO 4.4 2.9 - - - -
110A VAL* 3.6 36.7 - - + +
114A ASP* 3.4 41.3 - - + +
133A LEU* 4.4 6.1 - - + +
138A ALA 4.4 0.3 - - - +
139A SER* 3.4 2.1 - - - -
140A ILE* 2.9 39.0 + - + +
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Residues in contact with SER 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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104A LYS* 1.3 90.7 + - - +
106A GLY* 1.3 67.1 + - - +
107A ILE 5.2 0.2 - - - +
133A LEU* 5.0 0.9 - - - -
136A GLU 5.2 2.2 - - - -
138A ALA 3.4 6.5 - - - -
139A SER* 3.0 26.9 - - - -
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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