Contacts of the strand formed by residues 136 - 140 (chain C) in PDB entry 4KGQ
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 ALA 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C CYS* 3.7 6.1 - - + +
133C PRO* 2.8 28.2 + - + +
135C GLY* 1.3 82.6 - - - +
137C GLY* 1.3 57.8 + - - +
150C CYS* 5.0 3.1 - - + -
151C GLN 3.1 21.3 - - - +
152C PRO* 4.1 3.1 - - + -
153C CYS* 3.7 8.8 - - - -
159C SER* 3.2 3.1 + - - -
301C MG 2.2 32.6 - - - -
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Residues in contact with GLY 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C CYS* 3.8 7.4 - - - -
136C ALA* 1.3 77.1 - - - +
138C VAL* 1.3 66.1 + - - -
139C ILE* 3.5 0.6 + - - -
150C CYS* 3.3 0.7 - - - -
151C GLN* 2.9 36.5 + - - +
159C SER* 4.7 0.2 - - - -
166C GLU 3.6 9.6 - - - -
167C GLN* 4.3 0.9 - - - -
168C CYS* 3.4 22.4 - - - -
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Residues in contact with VAL 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C CYS* 3.8 15.3 - - - -
137C GLY* 1.3 72.8 - - - -
139C ILE* 1.3 63.6 + - - +
140C ALA* 3.7 28.3 - - - +
141C PRO* 3.9 12.8 - - + -
148C THR* 4.0 4.3 - - + -
149C GLN 3.3 7.2 - - - +
163C SER 4.0 2.5 - - - +
164C SER 3.7 24.9 - - - +
165C SER* 3.7 17.5 - - - +
166C GLU 3.1 18.6 + - - +
167C GLN* 3.8 27.0 + - + +
168C CYS 4.8 0.5 + - - -
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Residues in contact with ILE 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C GLY 3.5 1.1 + - - +
138C VAL* 1.3 77.2 - - - +
140C ALA* 1.3 63.2 + - + +
141C PRO* 4.8 0.9 - - - +
149C GLN* 2.9 24.2 + - + +
150C CYS 3.9 15.3 - - - +
151C GLN* 3.6 45.3 - - + +
167C GLN* 5.7 1.3 - - - +
145D SER* 4.0 28.0 - - - +
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Residues in contact with ALA 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C VAL* 3.7 7.6 - - - +
139C ILE* 1.3 84.2 - - - +
141C PRO* 1.3 78.2 - - + +
146C GLN* 4.3 8.5 - - - +
148C THR* 3.8 0.9 - - - -
149C GLN* 3.0 45.1 + - + +
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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