Contacts of the helix formed by residues 135 - 143 (chain B) in PDB entry 4GJC
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 PRO 135 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B SER* 3.7 25.4 - - - +
38B VAL* 5.9 0.2 - - + -
99B GLN* 3.9 2.2 - - - +
122B GLY 4.6 4.9 - - - +
124B GLY 3.9 17.3 - - - +
125B PHE 4.0 1.6 - - - -
126B ILE* 3.6 33.7 - - + +
133B VAL 3.3 7.2 - - - +
134B THR* 1.4 86.9 - - + +
136B ILE* 1.3 66.1 + - - +
137B PHE* 3.3 3.6 - - + +
138B ASP* 3.1 38.7 + - - +
139B ASN* 3.2 9.9 + - - -
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Residues in contact with ILE 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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18B ILE* 5.9 0.4 - - + -
38B VAL* 4.2 10.7 - - + +
89B ILE* 3.8 31.9 - - + -
91B VAL* 4.1 12.1 - - + -
96B VAL* 3.7 24.7 - - + -
99B GLN* 3.2 29.2 + - + +
121B VAL* 3.5 34.1 - - + -
122B GLY 4.1 10.0 + - - +
123B MET* 4.4 8.3 - - + -
135B PRO* 1.3 71.1 - - - +
137B PHE* 1.4 60.3 + - - +
139B ASN* 3.2 2.8 + - - +
140B ILE* 2.9 42.0 + - + +
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Residues in contact with PHE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLY 5.3 0.2 + - - -
123B MET* 4.3 20.9 - - + +
124B GLY 5.9 1.3 - - - +
135B PRO* 3.3 3.7 - - + +
136B ILE* 1.4 77.8 - - - +
138B ASP* 1.4 63.6 + - - +
140B ILE* 3.2 10.6 + - + +
141B ILE* 2.9 62.6 + - + +
146B LEU* 3.6 30.1 - - + -
149B ASP* 3.7 12.3 - - - -
150B VAL 3.6 27.1 - - - -
151B PHE* 3.7 38.4 - + + -
167B LEU* 4.2 18.8 - - + -
315B ARG* 4.0 16.8 - - + +
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Residues in contact with ASP 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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124B GLY 4.7 0.2 - - - +
126B ILE* 4.3 15.2 + - - +
134B THR* 3.8 14.6 - - + +
135B PRO* 3.1 33.7 + - - +
137B PHE* 1.4 74.2 - - - +
139B ASN* 1.3 58.2 + - - +
141B ILE* 3.4 11.3 + - - +
142B SER* 3.0 32.1 + - - -
315B ARG* 2.9 38.5 + - - -
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Residues in contact with ASN 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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96B VAL* 3.5 21.6 - - + +
97B THR 3.5 13.9 + - - -
99B GLN* 2.6 30.3 + - - +
100B MET 5.0 1.2 - - - +
134B THR* 3.2 32.6 + - - +
135B PRO 3.2 5.5 + - - -
136B ILE 3.2 6.7 + - - +
138B ASP* 1.3 75.9 - - - +
140B ILE* 1.4 58.8 + - - +
142B SER* 3.4 21.1 + - - -
143B GLN* 3.5 13.5 + - - +
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Residues in contact with ILE 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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91B VAL* 4.1 20.0 - - + -
94B ILE* 4.1 27.6 - - + -
96B VAL* 4.1 16.2 - - + -
136B ILE* 2.9 38.7 + - + +
137B PHE* 3.2 13.7 + - + +
139B ASN* 1.4 73.3 - - - +
141B ILE* 1.4 64.3 + - - +
143B GLN* 3.2 23.5 + - - +
144B GLY 3.9 1.9 + - - -
145B VAL* 4.7 4.8 + - + +
146B LEU* 3.7 32.0 - - + +
167B LEU* 4.3 16.2 - - + -
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Residues in contact with ILE 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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-5B LEU* 3.7 32.3 - - + -
-4B THR 3.9 7.4 + - - +
137B PHE* 2.9 45.0 + - + +
138B ASP* 3.6 13.0 - - - +
140B ILE* 1.4 75.1 - - - +
142B SER* 1.4 53.7 + - - +
144B GLY* 2.8 28.6 + - - -
146B LEU* 5.1 7.2 - - + -
149B ASP* 2.9 34.5 - - + +
315B ARG* 4.4 17.3 - - + +
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Residues in contact with SER 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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-4B THR* 5.3 4.2 + - - -
138B ASP 3.0 18.1 + - - -
139B ASN* 3.4 16.7 + - - -
140B ILE 3.3 0.2 - - - -
141B ILE* 1.4 74.9 - - - +
143B GLN* 1.4 58.8 + - - +
144B GLY* 3.4 1.4 + - - -
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Residues in contact with GLN 143 (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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94B ILE* 4.1 9.5 - - - +
95B THR 2.7 29.5 + - - +
96B VAL* 3.5 23.9 - - - +
97B THR 4.9 0.4 - - - +
139B ASN 3.7 10.8 - - - +
140B ILE* 3.2 12.6 + - - +
141B ILE 3.0 1.2 + - - -
142B SER* 1.4 75.3 - - - +
144B GLY* 1.3 62.0 + - - +
145B VAL* 3.4 30.0 + - + +
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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