Contacts of the helix formed by residues 140 - 155 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136D SER* 2.8 18.4 + - - +
139D ARG* 1.3 78.9 - - + +
141D LYS* 1.3 64.2 + - - +
142D ALA* 3.6 12.1 - - - +
143D GLU* 2.9 53.4 + - + +
144D TYR 2.9 10.0 + - - -
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Residues in contact with LYS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D SER 3.3 5.7 + - - -
137D PHE* 4.7 11.5 + - + +
139D ARG 4.0 0.6 - - - -
140D ASN* 1.3 72.9 - - - +
142D ALA* 1.3 53.8 + - - +
144D TYR* 3.4 6.8 - - + +
145D ASP* 2.8 64.8 + - - +
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D ASN* 3.2 10.8 - - - +
141D LYS* 1.3 79.6 - - - +
143D GLU* 1.3 57.4 + - - +
145D ASP* 3.9 7.5 - - - +
146D LYS* 3.1 28.1 + - - +
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Residues in contact with GLU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D TYR* 5.0 0.7 - - - +
136D SER* 2.9 24.5 + - - +
140D ASN* 2.9 33.1 + - - +
142D ALA* 1.3 76.6 - - - +
144D TYR* 1.3 67.7 + - - +
146D LYS* 3.3 10.4 + - + +
147D LYS* 3.2 28.7 + - + +
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Residues in contact with TYR 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D TRP* 4.2 12.6 - + - -
82D TYR* 3.7 24.2 - + - -
83D HIS* 4.3 1.4 - - - -
84D PRO* 3.2 31.1 - - + +
120D LEU 4.6 1.2 + - - -
123D PRO* 3.8 8.8 - - + +
133D ALA 3.5 25.8 - - - -
136D SER* 3.7 23.2 - - - +
137D PHE* 3.6 31.4 - + + -
140D ASN 2.9 4.9 + - - -
141D LYS* 3.4 10.5 - - + +
143D GLU* 1.3 75.9 - - - +
145D ASP* 1.3 76.8 + - - +
147D LYS* 3.2 5.4 + - - +
148D VAL* 3.1 42.1 + - + +
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Residues in contact with ASP 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ASN* 3.8 24.7 + - - +
141D LYS* 2.8 55.8 + - - +
142D ALA* 3.9 6.4 - - - +
144D TYR* 1.3 87.8 - - - +
146D LYS* 1.3 58.8 + - - +
148D VAL* 3.3 6.8 + - - +
149D LEU* 2.9 39.9 + - + +
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LYS 4.5 3.6 - - - -
154A GLN* 2.7 45.0 + - + +
156A SER 4.7 8.1 + - - -
142D ALA 3.1 17.9 + - - +
143D GLU* 3.7 9.2 - - + +
144D TYR 3.3 0.2 - - - -
145D ASP* 1.3 76.0 - - - +
147D LYS* 1.3 64.8 + - + +
149D LEU* 3.4 10.3 + - - +
150D LEU* 3.0 40.7 + - + +
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Residues in contact with LYS 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLY 5.5 4.6 + - - -
154A GLN* 3.3 40.5 + - + +
82D TYR* 3.5 51.6 - - + +
143D GLU* 3.2 16.0 + - + +
144D TYR 3.2 3.6 + - - +
146D LYS* 1.3 78.8 - - + +
148D VAL* 1.3 60.1 + - - +
150D LEU* 3.3 8.2 + - + +
151D GLN* 2.9 30.6 + - - +
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Residues in contact with VAL 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ASN* 3.7 19.7 - - + +
53D TRP* 3.4 50.9 - - + +
58D TYR* 5.0 0.2 + - - -
82D TYR* 4.4 8.5 - - + -
144D TYR* 3.1 45.0 + - + +
145D ASP* 3.3 8.9 + - - +
147D LYS* 1.3 75.7 - - - +
149D LEU* 1.3 56.9 + - - +
151D GLN* 3.2 9.8 + - - +
152D ALA* 2.8 28.1 + - - +
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Residues in contact with LEU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ASN* 3.6 48.5 - - + +
145D ASP* 2.9 29.7 + - + +
146D LYS* 3.9 7.2 - - - +
147D LYS 3.3 0.2 - - - -
148D VAL* 1.3 77.0 - - - +
150D LEU* 1.3 61.8 + - + +
152D ALA* 3.4 4.3 + - + +
153D LYS* 3.2 21.7 + - - +
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Residues in contact with LEU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 3.8 22.3 - - + +
153A LYS* 3.7 40.4 - - + +
154A GLN* 3.7 41.1 - - + -
146D LYS* 3.0 36.3 + - + +
147D LYS* 3.7 8.5 - - + +
149D LEU* 1.3 73.7 - - + +
151D GLN* 1.3 60.6 + - - +
153D LYS* 3.3 7.7 + - - +
154D GLN* 2.8 26.2 + - - +
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Residues in contact with GLN 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D TRP* 3.4 24.4 - - + -
58D TYR* 4.0 3.3 - - + -
80D GLY 4.9 0.3 - - - +
81D PHE* 3.5 21.4 - - + -
82D TYR* 2.8 56.8 + - + +
147D LYS* 2.9 17.5 + - + +
148D VAL* 3.6 5.1 - - - +
150D LEU* 1.3 72.7 - - - +
152D ALA* 1.3 66.9 + - - +
154D GLN* 3.1 15.8 + - - +
155D TYR* 3.0 40.0 + - + -
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ASN 3.5 23.6 - - - +
53D TRP* 4.0 0.4 - - - +
54D ALA 3.8 15.3 - - - +
56D GLY* 3.6 4.0 - - - +
58D TYR* 3.3 26.2 + - - +
148D VAL 2.8 8.0 + - - +
149D LEU* 3.5 9.0 - - + +
151D GLN* 1.3 76.9 - - - +
153D LYS* 1.3 56.4 + - - +
155D TYR 3.2 3.8 + - - -
156D SER* 2.9 30.3 + - - -
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Residues in contact with LYS 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LYS* 3.7 10.9 + - - -
150A LEU* 4.0 13.9 - - + -
153A LYS* 3.0 35.9 - - - +
149D LEU 3.2 12.5 + - - +
150D LEU* 3.4 10.1 - - + +
152D ALA* 1.3 73.0 - - - +
154D GLN* 1.3 66.8 + - - +
156D SER* 3.1 24.9 + - - +
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Residues in contact with GLN 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LYS* 3.3 22.4 + - + +
147A LYS* 3.5 41.7 - - + +
150A LEU* 3.7 23.7 - - + +
150D LEU 2.8 14.6 + - - +
151D GLN* 3.1 20.6 + - - +
153D LYS* 1.3 76.3 - - - +
155D TYR* 1.3 93.3 + - + +
156D SER 4.6 0.2 - - - +
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Residues in contact with TYR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LYS* 5.2 3.3 + - - -
56D GLY* 3.9 1.1 - - - -
57D VAL* 2.9 35.5 + - - +
58D TYR* 3.6 28.9 - + + -
59D PRO* 3.4 33.9 - - + -
78D PRO* 3.5 24.5 - - + +
81D PHE* 3.8 22.5 - + - +
151D GLN* 3.0 27.5 + - + -
152D ALA 3.5 3.1 - - - -
154D GLN* 1.3 109.3 + - + +
156D SER* 1.3 62.9 + - - +
157D LYS* 4.1 0.3 + - - +
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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