Contacts of the helix formed by residues 140 - 155 (chain B) in PDB entry 2GJD
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 ASN 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B SER* 2.8 15.4 + - - +
139B ARG* 1.3 83.1 - - + +
141B LYS* 1.3 63.9 + - - +
142B ALA* 3.7 11.7 - - - +
143B GLU* 3.1 44.7 + - - +
144B TYR 3.1 14.0 + - - -
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Residues in contact with LYS 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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52B ASN* 5.6 0.6 - - - +
136B SER 3.3 3.8 + - - -
137B PHE* 3.5 55.3 + - + +
138B SER 5.6 0.2 - - - -
139B ARG 4.0 0.6 - - - -
140B ASN* 1.3 75.2 - - - +
142B ALA* 1.3 56.6 + - - +
144B TYR* 3.2 11.5 + - + +
145B ASP* 2.9 63.3 + - - +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ASN* 3.2 10.4 + - - +
141B LYS* 1.3 77.0 - - - +
143B GLU* 1.3 57.1 + - - +
145B ASP* 3.5 8.0 + - - +
146B LYS* 3.1 28.2 + - - +
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Residues in contact with GLU 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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136B SER* 2.6 28.2 + - - +
140B ASN* 3.1 34.8 + - - +
142B ALA* 1.3 75.9 - - - +
144B TYR* 1.3 65.5 + - - +
146B LYS* 3.3 8.1 + - - +
147B LYS* 3.1 50.4 + - - +
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Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TRP* 4.0 18.6 - + - -
82B TYR* 3.4 36.6 - + - -
83B HIS* 4.6 0.5 - - - -
84B PRO* 3.3 30.9 - - + +
120B LEU 4.4 0.7 + - - -
123B PRO* 3.9 9.8 - - + +
133B ALA* 3.7 19.7 - - + -
136B SER* 3.9 2.9 - - - +
137B PHE* 3.7 35.0 - + + +
140B ASN 3.1 5.9 + - - +
141B LYS* 3.2 28.5 + - - +
143B GLU* 1.3 79.6 - - - +
145B ASP* 1.3 68.0 + - - +
147B LYS* 3.2 4.9 + - - +
148B VAL* 3.0 42.4 + - + +
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Residues in contact with ASP 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASN* 3.5 27.2 + - - +
141B LYS* 2.9 54.5 + - - +
142B ALA* 3.8 7.1 - - - +
144B TYR* 1.3 82.3 - - - +
146B LYS* 1.3 57.5 + - - +
148B VAL* 3.2 4.4 + - - +
149B LEU* 2.9 38.9 + - + +
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Residues in contact with LYS 146 (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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142B ALA 3.1 17.2 + - - +
143B GLU* 3.6 8.5 - - - +
145B ASP* 1.3 75.5 - - - +
147B LYS* 1.3 58.7 + - + +
149B LEU* 3.5 10.4 + - + +
150B LEU* 3.0 52.8 + - + +
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Residues in contact with LYS 147 (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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82B TYR* 3.6 44.9 + - + +
132B PRO* 6.0 3.2 - - - +
136B SER* 4.8 2.4 + - - -
143B GLU* 3.1 41.7 + - - +
144B TYR 3.5 5.6 - - - +
146B LYS* 1.3 76.8 - - + +
148B VAL* 1.3 56.2 + - - +
150B LEU* 3.3 9.4 + - + +
151B GLN* 2.8 31.7 + - - +
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASN* 3.6 29.8 - - + +
53B TRP* 3.5 41.5 - - + +
58B TYR* 4.9 0.7 + - - -
82B TYR* 4.4 6.5 - - + -
144B TYR* 3.0 49.4 + - + +
145B ASP* 3.6 8.5 - - - +
147B LYS* 1.3 75.2 - - - +
149B LEU* 1.3 56.7 + - - +
151B GLN* 3.2 9.8 + - - +
152B ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 149 (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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51B THR 5.4 0.4 - - - +
52B ASN* 3.5 44.4 - - + +
145B ASP* 2.9 27.1 + - + +
146B LYS* 3.7 9.0 - - + +
148B VAL* 1.3 77.7 - - - +
150B LEU* 1.3 64.4 + - + +
152B ALA* 3.4 5.2 + - + +
153B LYS* 3.3 29.0 + - - +
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Residues in contact with LEU 150 (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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146B LYS* 3.0 42.0 + - + +
147B LYS* 3.9 7.0 - - + +
149B LEU* 1.3 75.3 - - + +
151B GLN* 1.3 61.8 + - - +
153B LYS* 3.2 33.3 + - + +
154B GLN* 2.9 24.8 + - - +
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Residues in contact with GLN 151 (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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53B TRP* 3.3 24.9 - - - -
58B TYR* 3.9 4.2 - - + -
80B GLY 4.9 0.2 - - - +
81B PHE* 3.6 18.2 - - + -
82B TYR* 2.9 57.7 + - + +
147B LYS 2.8 17.5 + - - +
148B VAL* 3.6 6.2 - - - +
150B LEU* 1.3 73.6 - - - +
152B ALA* 1.3 64.9 + - - +
154B GLN* 3.2 17.3 + - - +
155B TYR* 3.1 39.6 + - + +
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Residues in contact with ALA 152 (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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52B ASN 3.8 10.1 - - - +
53B TRP 4.0 0.2 - - - +
54B ALA 3.7 21.5 - - - +
55B GLY 4.2 1.0 - - - -
56B GLY* 3.5 5.4 + - - +
58B TYR* 3.3 25.5 + - - +
148B VAL 2.9 12.2 + - - +
149B LEU* 3.5 11.0 - - + +
150B LEU 3.2 0.2 - - - -
151B GLN* 1.3 77.8 - - - +
153B LYS* 1.3 55.8 + - + +
155B TYR 3.4 3.5 - - - -
156B SER* 3.0 27.2 + - - -
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Residues in contact with LYS 153 (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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149B LEU* 3.3 18.3 + - - +
150B LEU* 3.2 32.9 + - + +
152B ALA* 1.3 75.6 - - + +
154B GLN* 1.3 65.3 + - - +
156B SER* 3.0 26.9 + - - -
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Residues in contact with GLN 154 (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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150B LEU 2.9 12.9 + - - +
151B GLN* 3.2 23.3 + - - +
153B LYS* 1.3 77.1 - - - +
155B TYR* 1.3 93.7 + - + +
156B SER* 3.6 2.3 + - - -
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Residues in contact with TYR 155 (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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57B VAL* 2.8 29.6 + - - +
58B TYR* 3.7 26.9 - + + -
59B PRO* 3.4 31.4 - - + -
78B PRO* 3.4 25.2 - - + +
81B PHE* 3.7 25.5 + + - -
151B GLN* 3.1 28.0 + - + +
152B ALA 3.4 2.9 - - - -
154B GLN* 1.3 110.1 + - + +
156B SER* 1.3 70.0 + - - +
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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