Contacts of the strand formed by residues 124 - 128 (chain A) in PDB entry 1KPI
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 LYS 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A ARG* 6.4 2.2 - - - +
91A VAL* 4.3 23.6 - - + -
98A VAL* 3.7 8.5 - - + -
115A PHE* 3.2 56.0 + - + +
118A VAL* 2.7 40.1 + - - +
120A SER* 3.6 30.0 - - - +
122A ARG 3.8 6.9 + - - +
123A ARG* 1.3 77.6 - - - +
125A GLU* 1.3 58.7 + - - +
126A VAL* 4.0 0.5 + - - +
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Residues in contact with GLU 125 (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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87A MET* 2.9 9.1 - - - +
98A VAL 2.8 14.6 + - - +
99A ILE* 3.3 19.2 - - + +
100A GLY 2.5 32.9 + - - -
123A ARG* 3.0 40.0 + - + -
124A LYS* 1.3 74.4 - - - +
126A VAL* 1.3 54.9 + - - +
127A ARG* 3.2 32.5 + - + +
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Residues in contact with VAL 126 (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 CYS* 4.1 12.3 - - - -
87A MET* 4.7 1.6 - - + -
100A GLY 3.4 7.4 - - - +
102A THR* 4.1 8.5 - - + -
108A TYR* 3.0 37.0 + - + -
111A ASP* 3.9 28.7 - - + +
112A LYS* 4.0 29.8 - - + +
115A PHE* 4.3 10.1 - - + -
124A LYS 4.0 1.0 + - - +
125A GLU* 1.3 74.3 - - - +
127A ARG* 1.3 67.5 + - - +
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Residues in contact with ARG 127 (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* 3.7 24.7 - - + +
100A GLY 2.7 15.5 + - - +
101A LEU* 4.6 2.9 - - + -
102A THR* 3.1 30.7 + - - +
108A TYR* 4.1 5.2 - - - -
125A GLU* 3.2 28.7 + - + -
126A VAL* 1.3 82.3 - - - +
128A ILE* 1.3 63.8 + - - +
129A GLN* 3.1 37.9 + - + +
134A PHE* 3.5 8.7 - - - -
136A GLU* 2.5 44.8 + - - -
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Residues in contact with ILE 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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21A ARG* 3.5 24.9 - - - +
102A THR* 3.1 11.0 - - + +
103A LEU* 4.4 8.5 - - + +
104A SER 4.1 5.2 - - - +
105A GLU* 4.1 25.1 - - + +
108A TYR* 3.5 47.3 - - + -
127A ARG* 1.3 72.7 - - - +
129A GLN* 1.3 57.0 + - - +
133A GLU* 5.3 0.3 - - - +
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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