Contacts of the strand formed by residues 127 - 132 (chain A) in PDB entry 2KC2
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 TYR 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.6 34.8 - - + +
121A ILE* 4.5 10.8 - - + -
123A ASN* 3.2 45.8 - - - +
124A HIS* 2.8 39.4 + - - +
125A ASP 3.4 0.4 - - - -
126A GLU* 1.3 93.1 - - + +
128A SER* 1.3 60.0 + - - +
176A HIS* 5.2 1.4 - - - -
193A LEU* 3.7 30.1 - - + -
194A ARG 3.9 4.0 - - - -
195A ARG* 3.5 44.9 + - + -
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Residues in contact with SER 128 (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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124A HIS 5.5 0.4 - - - -
126A GLU 3.7 2.0 + - - -
127A TYR* 1.3 74.3 - - - +
129A LEU* 1.3 75.8 + - - +
173A TRP* 3.3 24.0 - - - -
174A LEU 3.6 11.8 + - - -
175A ASP* 3.8 17.1 + - - -
176A HIS* 5.7 3.2 - - - -
193A LEU* 3.3 12.8 - - - +
194A ARG 3.1 21.8 + - - +
196A LYS* 3.8 16.1 + - - -
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Residues in contact with LEU 129 (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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108A VAL* 4.5 4.5 - - + -
112A LEU* 3.5 38.8 - - + -
124A HIS* 4.1 9.9 - - + -
128A SER* 1.3 89.8 + - - +
130A VAL* 1.3 63.3 + - - +
173A TRP* 3.3 7.8 - - - -
174A LEU* 2.8 48.0 + - + +
176A HIS* 3.6 33.0 - - + +
191A LEU* 3.7 15.3 - - + -
192A LEU 3.6 1.1 - - - -
193A LEU* 3.6 24.0 - - + -
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Residues in contact with VAL 130 (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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129A LEU* 1.3 78.1 - - - +
131A ARG* 1.3 64.0 + - - +
132A GLU* 4.1 0.9 - - + +
170A GLU 4.2 1.6 - - - +
171A LEU* 3.7 30.7 - - + -
172A ASN 3.6 16.6 - - - +
173A TRP* 3.4 36.3 - - + +
174A LEU* 3.7 4.5 - - - -
191A LEU* 3.5 5.4 - - - +
192A LEU* 2.8 68.0 + - + +
194A ARG* 4.6 1.3 - - + -
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Residues in contact with ARG 131 (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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130A VAL* 1.3 68.9 - - - +
132A GLU* 1.3 61.6 + - - +
133A LEU* 3.3 18.2 + - + +
170A GLU 2.8 16.1 - - - +
172A ASN* 2.6 44.7 + - + +
174A LEU* 3.7 22.2 - - + +
180A LEU* 5.9 0.2 - - + -
183A GLN* 5.3 6.5 + - - -
184A GLY 5.7 1.3 + - - -
185A VAL* 3.5 43.2 - - + +
189A GLU* 2.7 29.7 + - + +
190A THR 3.9 4.0 - - - -
191A LEU* 4.8 4.7 - - + -
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Residues in contact with GLU 132 (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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91A ARG* 2.6 55.8 + - - +
97A VAL* 5.6 2.6 - - - +
130A VAL* 3.3 2.7 + - - -
131A ARG* 1.3 69.5 - - - +
133A LEU* 1.3 73.7 + - - +
134A MET* 3.4 6.4 + - - +
170A GLU* 3.4 14.4 - - + +
189A GLU* 4.5 3.5 - - - +
190A THR* 2.7 58.6 + - - +
192A LEU* 3.6 18.3 - - + +
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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