Contacts of the strand formed by residues 128 - 134 (chain B) in PDB entry 4KYI
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 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B GLN 2.9 20.1 + - - +
96B ALA* 3.6 6.1 - - - +
97B ALA 3.4 15.5 + - - -
126B ASN 4.5 5.4 - - - +
127B ILE* 1.3 70.0 - - - +
129B ILE* 1.3 65.4 + - - +
130B ALA* 3.4 2.4 + - - +
159B LEU* 5.0 2.5 - - + -
178B ILE* 3.7 27.7 - - + +
181B LYS* 3.7 46.9 - - + +
182B LEU* 3.7 20.2 - - + -
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ALA* 3.5 9.0 - - + +
99B VAL* 4.3 6.5 - - + -
116B VAL* 4.5 6.5 - - + +
119B LEU* 3.7 41.7 - - + -
120B GLN* 4.2 22.0 - - + +
127B ILE* 3.2 31.7 + - + +
128B VAL* 1.3 74.1 - - - +
130B ALA* 1.3 71.2 + - - +
157B SER 4.7 2.6 - - - +
158B LEU* 3.6 32.3 - - + -
159B LEU* 3.5 18.4 + - - +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ALA 2.7 15.6 + - - +
98B ILE* 4.4 4.5 - - - -
99B VAL* 3.0 30.6 + - - +
128B VAL 3.4 0.6 + - - -
129B ILE* 1.3 78.2 - - - +
131B LEU* 1.3 59.8 + - - +
158B LEU* 4.9 0.8 - - - +
159B LEU* 3.7 21.1 - - + +
174B ILE* 4.2 15.3 - - + -
178B ILE* 3.9 27.8 - - + -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL* 3.4 25.6 - - + +
101B TYR* 3.7 26.2 - - + -
109B PHE* 4.5 11.7 - - + -
112B ALA* 4.5 9.6 - - + -
116B VAL* 5.3 2.5 - - + -
130B ALA* 1.3 75.2 - - - +
132B ALA* 1.3 64.9 + - - +
149B ALA* 4.3 7.0 - - + +
152B TYR* 4.5 7.9 - - + -
153B ALA* 4.1 11.7 - - + -
158B LEU* 3.8 31.6 - - + -
159B LEU 3.0 21.1 + - - +
160B PHE* 3.8 22.4 - - + -
161B MET 3.2 15.4 + - - -
174B ILE* 4.0 3.3 - - - +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 5.2 1.8 - - + -
98B ILE* 4.3 10.3 - - + -
99B VAL 3.0 12.0 + - - +
100B VAL* 3.6 10.0 - - + -
101B TYR* 3.0 34.9 + - - -
131B LEU* 1.3 76.9 - - - +
133B GLY* 1.3 59.1 + - - +
134B ASN 3.7 0.6 + - - -
161B MET 3.7 4.0 - - - -
163B THR* 4.1 17.7 - - + +
174B ILE* 3.7 21.8 - - + -
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TYR* 3.5 31.2 - - - -
103B ILE* 3.9 10.5 - - - +
132B ALA* 1.3 70.5 - - - +
134B ASN* 1.3 65.1 + - - +
136B ALA* 3.9 3.6 - - - +
160B PHE* 3.9 2.1 - - - -
161B MET 3.2 13.4 + - - -
162B GLU* 3.5 8.5 - - - +
163B THR 3.2 19.5 + - - +
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Residues in contact with ASN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B VAL 3.1 17.9 + - - +
33B GLY* 3.9 3.2 - - - -
37B LEU* 3.2 22.6 - - - +
100B VAL* 3.8 11.7 - - + -
101B TYR 3.0 15.0 + - - +
102B ASP* 3.7 0.5 - - - +
103B ILE* 3.4 19.1 + - - +
132B ALA 3.7 0.8 + - - -
133B GLY* 1.3 74.5 - - - +
135B LYS* 1.3 76.8 + - - +
136B ALA 3.2 1.8 - - - -
163B THR* 2.3 36.9 + - - +
301B GNP 2.7 42.8 + - - +
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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