Contacts of the strand formed by residues 97 - 109 (chain A) in PDB entry 2KLR
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LYS* 4.0 1.2 - - - +
93A VAL* 3.4 4.4 - - - +
94A LEU* 2.8 61.3 + - + +
95A GLY 4.7 0.9 - - - -
96A ASP* 1.3 99.3 - - - +
98A ILE* 1.3 60.4 + - - +
99A GLU* 3.9 24.9 - - + +
122A TYR 3.3 15.0 - - - +
123A ARG* 3.9 11.4 - - + -
128A VAL* 5.2 0.7 - - - -
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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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77A VAL* 5.4 0.2 - - + -
79A LEU* 4.2 13.8 - - + +
91A VAL* 4.3 11.7 - - + -
92A LYS 3.3 18.2 - - - +
93A VAL* 3.7 22.0 - - + -
97A VAL* 1.3 74.6 - - - +
99A GLU* 1.3 62.1 + - - +
121A LYS 3.9 0.2 - - - -
122A TYR* 3.0 54.6 + - + +
124A ILE* 3.8 22.2 - - + -
128A VAL* 3.9 13.9 - - + -
135A SER* 4.5 0.4 - - - +
145A VAL* 3.5 38.8 - - + -
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Residues in contact with GLU 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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79A LEU* 5.1 0.9 - - - -
91A VAL* 4.0 1.0 - - - +
92A LYS* 2.7 76.9 + - + +
97A VAL* 3.9 19.5 - - + +
98A ILE* 1.3 85.0 - - - +
100A VAL* 1.3 67.9 + - - +
119A HIS* 2.6 34.4 + - + +
120A ARG 3.2 8.7 - - - +
121A LYS* 4.0 14.2 - - + +
122A TYR 4.4 1.8 - - - +
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 3.7 24.2 - - + -
81A VAL* 4.2 18.6 - - + -
89A LEU* 4.3 9.6 - - + -
90A LYS 3.5 4.3 - - - +
91A VAL* 3.8 10.5 - - + -
98A ILE* 5.5 0.2 - - + -
99A GLU* 1.3 81.6 - - - +
101A HIS* 1.3 60.8 + - - +
118A PHE 3.6 0.6 - - - +
119A HIS* 3.2 9.5 - - - -
120A ARG* 3.0 52.2 + - + +
143A LEU* 3.5 33.2 - - + -
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Residues in contact with HIS 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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88A GLU 3.9 0.3 - - - +
89A LEU* 3.4 4.6 - - - +
90A LYS* 2.7 55.5 + - + +
92A LYS* 5.4 8.2 - - + +
100A VAL* 1.3 75.9 - - - +
102A GLY* 1.3 64.1 + - - +
103A LYS* 3.7 30.3 + - + -
117A GLU* 2.6 31.4 + - + -
118A PHE 3.5 5.4 - - - -
119A HIS* 4.5 19.7 - + + -
117B GLU* 5.8 0.7 - - - -
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Residues in contact with GLY 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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81A VAL* 5.6 0.2 - - - -
84A PHE* 3.4 20.4 - - - -
88A GLU 3.0 10.3 - - - -
89A LEU* 4.0 7.9 - - - +
101A HIS* 1.3 78.8 + - - +
103A LYS* 1.3 60.4 + - - +
117A GLU* 3.2 6.8 - - - +
118A PHE* 2.7 37.6 + - - +
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Residues in contact with LYS 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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84A PHE* 3.8 0.8 - - - -
88A GLU* 2.9 31.1 + - - +
101A HIS* 3.7 19.5 - - + -
102A GLY* 1.3 75.6 - - - +
104A HIS* 1.3 66.6 + - - +
115A SER* 5.2 7.4 - - - -
116A ARG 3.5 5.6 - - - +
117A GLU* 3.7 26.9 - - + +
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Residues in contact with HIS 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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84A PHE* 3.3 30.0 - + + -
85A SER* 6.0 2.6 + - - -
88A GLU* 4.1 23.6 + - + +
103A LYS* 1.3 76.7 - - - +
105A GLU* 1.3 82.5 + - + +
106A GLU* 3.1 28.7 + - - +
115A SER* 3.3 5.4 - - - -
116A ARG* 2.8 41.4 + - - +
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Residues in contact with GLU 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 HIS* 1.3 94.2 + - + +
106A GLU* 1.3 65.0 + - - +
108A GLN* 3.6 33.0 + - + +
113A PHE* 3.6 12.7 - - - +
114A ILE 2.8 19.3 + - - +
115A SER* 2.6 22.2 + - - +
121B LYS* 2.7 27.8 + - - -
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Residues in contact with GLU 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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104A HIS* 3.1 21.4 + - - +
105A GLU* 1.3 76.0 - - - +
107A ARG* 1.3 79.7 + - + +
108A GLN* 5.6 0.4 - - - -
114A ILE* 2.6 21.1 + - + +
115A SER 3.8 3.6 - - - +
116A ARG* 2.8 73.8 + - + +
82B LYS* 5.1 6.9 + - - -
118B PHE* 4.4 13.2 - - + -
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Residues in contact with ARG 107 (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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106A GLU* 1.3 93.8 + - + +
108A GLN* 1.3 65.3 + - - +
109A ASP* 5.2 0.7 - - + -
113A PHE 3.6 0.3 - - - -
114A ILE* 2.8 64.4 + - + +
80B ASP* 2.6 48.0 + - - -
82B LYS* 4.7 17.8 - - - +
118B PHE* 5.1 5.9 - - - -
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Residues in contact with GLN 108 (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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105A GLU* 3.6 31.3 + - + +
106A GLU 5.6 0.2 - - - -
107A ARG* 1.3 76.0 - - - +
109A ASP* 1.3 61.8 + - - +
112A GLY 3.9 3.1 - - - -
113A PHE* 3.7 28.9 - - + -
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Residues in contact with ASP 109 (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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107A ARG* 5.4 1.1 - - + -
108A GLN* 1.3 75.2 - - - +
110A GLU* 1.4 73.5 + - + +
111A HIS* 2.9 2.6 + - - -
112A GLY 2.7 31.8 + - - +
113A PHE* 4.4 6.9 - - - -
114A ILE* 4.1 8.5 - - + +
120B ARG* 2.9 34.4 + - - -
122B TYR* 2.6 28.8 + - - -
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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