Contacts of the strand formed by residues 136 - 142 (chain B) in PDB entry 2GPC
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 LEU 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL* 5.1 1.3 - - + +
97B GLU* 4.0 35.4 - - + +
98B ILE* 4.0 18.6 - - + -
101B SER* 2.9 25.9 + - - +
102B PHE* 3.7 18.3 - - + -
127B LEU* 4.0 9.9 - - + -
128B VAL 3.3 4.9 - - - +
129B LYS* 3.6 37.5 - - + -
134B GLY 4.1 1.8 - - - +
135B LYS* 1.3 84.4 - - - +
137B LYS* 1.3 66.3 + - - +
156B LEU* 3.7 27.6 - - + -
194B LEU* 5.0 2.2 - - + -
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Residues in contact with LYS 137 (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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102B PHE* 3.9 10.3 - - - -
127B LEU* 3.5 3.5 - - - +
128B VAL* 3.0 45.1 + - + +
130B ASP* 2.9 37.7 + - + +
133B SER* 5.3 0.6 + - - -
135B LYS* 4.3 20.2 - - + +
136B LEU* 1.3 81.1 - - - +
138B VAL* 1.3 68.3 + - - +
139B TYR* 5.4 1.1 - - + -
153B LEU* 5.7 4.4 - - + +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 3.8 25.6 - - + -
108B PHE* 4.2 13.2 - - + -
111B GLU* 3.6 26.0 + - + +
112B PHE* 4.0 30.5 - - + +
115B VAL* 3.8 38.4 - - + -
126B TRP 3.4 9.2 - - - +
137B LYS* 1.3 76.8 - - - +
139B TYR* 1.3 64.3 + - - +
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Residues in contact with TYR 139 (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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115B VAL* 4.9 0.2 - - - -
125B ALA* 3.9 0.6 - - - -
126B TRP* 2.7 39.6 + + - +
128B VAL* 3.9 29.4 - - + -
137B LYS* 5.4 0.9 - - + -
138B VAL* 1.3 80.2 - - - +
140B GLN* 1.3 68.2 + - - +
141B THR* 3.4 28.0 - - + +
146B CYS 5.2 0.7 + - - -
147B PRO* 4.1 23.2 - - + +
149B THR* 5.5 0.2 + - - -
150B GLU* 3.2 27.2 - - + +
153B LEU* 4.0 22.7 - - + -
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Residues in contact with GLN 140 (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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115B VAL* 3.7 35.1 - - + +
119B HIS* 2.7 41.2 + - + +
124B TRP 3.3 11.4 - - - +
139B TYR* 1.3 87.3 - - - +
141B THR* 1.3 67.8 + - - +
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Residues in contact with THR 141 (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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119B HIS* 3.4 9.5 - - - -
123B GLY* 3.2 2.4 - - - -
124B TRP* 2.8 39.0 + - - +
126B TRP* 3.0 21.2 + - - +
139B TYR* 3.4 33.4 - - + +
140B GLN* 1.3 73.0 - - - +
142B HIS* 1.3 58.7 - - - +
145B GLY* 2.7 41.1 + - - +
146B CYS* 4.0 5.6 - - - +
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Residues in contact with HIS 142 (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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142A HIS* 3.7 6.1 + + - -
143A ASP* 2.7 38.1 + - - -
119B HIS* 2.8 24.8 + - + +
120B PHE 3.0 24.9 - - - -
122B SER 3.1 12.2 + - - -
141B THR* 1.3 75.0 - - - +
143B ASP* 1.3 93.0 + - - +
144B ALA 3.0 0.5 + - - -
145B GLY* 2.9 16.7 + - - -
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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