Contacts of the helix formed by residues 131 - 142 (chain B) in PDB entry 5GKI
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 SER 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B LEU* 4.3 18.8 + - - +
129B THR 3.5 1.2 - - - -
130B GLY* 1.3 79.7 - - - +
132B GLU* 1.3 64.3 + - - +
133B ALA* 3.8 11.2 - - - +
134B GLU* 2.9 35.2 + - - +
135B MET 3.3 13.7 + - - -
182B ARG* 4.5 7.2 - - - +
237B PRO* 4.2 6.2 - - - +
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Residues in contact with GLU 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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131B SER* 1.3 71.9 - - - +
133B ALA* 1.3 71.6 + - + +
134B GLU 3.1 0.9 - - - -
135B MET* 3.0 21.7 + - + +
136B ALA* 3.0 12.8 + - - +
156B GLU* 3.9 16.8 - - - +
165B ALA* 4.5 6.6 - - - +
179B GLU* 3.8 5.9 - - - +
180B LEU* 2.9 44.0 - - + +
181B LYS* 4.5 4.3 + - - -
182B ARG* 4.2 27.6 - - + +
103C MPD 6.1 0.3 - - - +
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Residues in contact with ALA 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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131B SER* 3.1 10.1 - - - +
132B GLU* 1.3 85.5 - - + +
134B GLU* 1.3 58.6 + - + +
136B ALA* 3.1 6.4 + - - +
137B GLU* 2.9 26.9 + - - +
155B ARG* 3.1 26.8 + - - +
103C MPD 5.9 7.0 - - + -
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Residues in contact with GLU 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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128B LEU 3.4 8.7 - - - +
129B THR* 2.8 43.0 + - - -
130B GLY 3.9 1.2 + - - -
131B SER* 2.9 28.8 + - - +
132B GLU 3.1 0.4 - - - -
133B ALA* 1.3 75.8 - - + +
135B MET* 1.3 58.5 + - - +
137B GLU* 3.7 23.4 - - - +
138B LEU* 2.9 27.2 + - - +
238B PRO* 3.7 20.3 - - + +
240B ARG* 4.5 6.0 + - - +
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Residues in contact with MET 135 (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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131B SER 3.3 6.4 + - - +
132B GLU* 3.0 15.8 + - - +
134B GLU* 1.3 77.2 - - - +
136B ALA* 1.3 62.0 + - - +
138B LEU* 3.1 8.0 + - - +
139B ILE* 3.0 27.9 + - + +
180B LEU* 4.2 13.9 - - + -
181B LYS 3.5 26.9 - - - +
182B ARG* 3.9 11.0 - - - -
213B VAL* 3.4 33.0 - - + +
235B LEU* 3.9 35.0 - - + +
237B PRO* 3.7 30.7 - - + -
238B PRO* 4.1 6.0 - - + +
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Residues in contact with ALA 136 (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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132B GLU* 3.0 11.9 + - - +
133B ALA* 3.1 10.3 + - - +
135B MET* 1.3 74.0 - - - +
137B GLU* 1.3 66.0 + - - +
139B ILE* 3.0 6.9 + - - +
140B PHE* 2.9 29.0 + - + -
155B ARG* 3.4 31.2 - - + +
165B ALA 5.8 0.2 - - - +
166B VAL* 4.5 7.6 - - + -
180B LEU* 4.0 18.8 - - + +
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Residues in contact with GLU 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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133B ALA* 2.9 14.1 + - - +
134B GLU* 3.7 26.4 - - - +
135B MET 3.3 0.2 - - - -
136B ALA* 1.3 75.1 - - - +
138B LEU* 1.3 62.3 + - - +
140B PHE* 3.5 3.3 + - - +
141B GLU* 3.0 43.6 + - + +
155B ARG* 3.8 29.7 + - - +
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Residues in contact with LEU 138 (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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134B GLU 2.9 14.6 + - - +
135B MET* 3.1 9.6 + - - +
137B GLU* 1.3 79.0 - - - +
139B ILE* 1.3 58.9 + - - +
141B GLU* 3.9 10.6 - - - +
142B ASN* 3.0 34.6 + - + +
145B VAL* 4.7 12.8 - - + -
235B LEU* 4.1 31.6 - - + -
236B GLU 4.8 1.1 - - - +
238B PRO* 4.3 27.8 - - + -
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Residues in contact with ILE 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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135B MET 3.0 17.2 + - - +
136B ALA* 3.0 10.6 + - - +
138B LEU* 1.3 77.3 - - - +
140B PHE* 1.3 65.3 + - + +
142B ASN 4.3 4.7 - - - -
143B PRO* 3.0 33.4 - - + +
145B VAL* 3.8 18.2 - - + -
146B ILE* 3.8 31.6 - - + -
150B PHE* 4.2 16.8 - - + -
152B PRO* 4.0 5.7 - - + +
166B VAL* 5.1 3.8 - - + -
178B LEU* 4.4 7.4 - - + -
180B LEU* 3.6 31.2 - - + -
235B LEU* 4.0 14.4 - - + -
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Residues in contact with PHE 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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136B ALA 2.9 22.1 + - - +
137B GLU* 4.2 4.7 - - - +
139B ILE* 1.3 80.4 - - + +
141B GLU* 1.3 60.1 + - + +
143B PRO* 4.3 7.1 - - - +
152B PRO* 3.7 45.6 - - + +
153B LEU 3.8 12.1 - - - -
154B PHE 3.2 34.8 - - - -
155B ARG* 4.0 21.8 - - + +
166B VAL* 3.8 20.4 - - + -
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Residues in contact with GLU 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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137B GLU* 3.0 36.1 + - - +
138B LEU* 4.0 11.0 - - + +
140B PHE* 1.3 78.8 - - + +
142B ASN* 1.3 67.2 + - + +
143B PRO* 3.8 4.6 - - - +
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Residues in contact with ASN 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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138B LEU* 3.0 21.2 + - + +
139B ILE 3.2 3.1 + - - -
141B GLU* 1.3 86.4 + - + +
143B PRO* 1.3 66.6 - - - +
144B GLU* 2.9 45.0 + - - +
145B VAL* 3.2 31.5 + - + +
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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