Contacts of the helix formed by residues 153 - 162 (chain A) in PDB entry 3GNI
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 HIS 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.9 33.6 + - + +
107A ARG* 5.1 2.5 - - + -
114A THR* 4.0 14.2 + - + -
117A VAL* 3.5 35.7 - - + +
149A GLU 3.6 18.5 + - - -
150A CYS 3.1 11.2 + - - +
152A ARG* 1.3 105.2 + - + +
154A GLU* 1.3 66.8 + - - +
155A PRO* 3.4 2.9 - - + -
156A LEU* 3.0 14.2 + - + -
157A ALA* 3.1 11.1 + - - +
195A HIS* 3.9 1.3 - - - -
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Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A HIS* 1.3 72.0 - - - +
155A PRO* 1.4 72.2 - - + +
157A ALA* 3.3 2.9 + - - +
158A LYS* 2.9 26.7 + - - +
195A HIS* 3.5 48.6 + - + +
197A LEU* 5.9 2.4 - - - +
198A LEU* 3.9 23.5 + - + +
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Residues in contact with PRO 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A VAL* 4.0 13.9 - - + -
121A CYS* 4.0 22.9 - - - -
153A HIS* 3.5 10.5 - - + -
154A GLU* 1.4 95.4 - - + +
156A LEU* 1.3 60.7 + - - +
158A LYS* 3.5 8.1 + - + +
159A ILE* 3.3 27.9 + - - +
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 4.2 10.3 - - + -
117A VAL* 4.0 20.2 - - + +
120A ILE* 3.7 46.7 - - + -
121A CYS* 4.0 22.0 - - - -
127A LEU* 3.9 20.9 - - + +
150A CYS* 3.5 40.8 - - + +
151A ILE* 4.7 3.1 - - - -
153A HIS* 3.0 6.1 + - + +
155A PRO* 1.3 73.9 - - - +
157A ALA* 1.3 66.1 + - - +
158A LYS 3.2 0.2 - - - -
159A ILE* 3.4 7.1 + - + +
160A ILE* 3.3 21.7 + - - +
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Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ILE* 3.7 26.0 - - - +
153A HIS 3.1 7.8 + - - +
154A GLU 3.4 8.7 - - - +
156A LEU* 1.3 76.1 - - - +
158A LYS* 1.3 55.5 + - - +
160A ILE* 3.4 3.3 + - - +
161A LEU* 3.0 32.1 + - + +
191A LEU* 4.0 21.2 - - + +
195A HIS* 4.0 9.6 - - - +
198A LEU* 3.8 15.0 - - + -
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Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLU* 2.9 19.6 + - - +
155A PRO* 3.7 8.7 - - + +
156A LEU 3.2 0.2 - - - -
157A ALA* 1.3 72.5 - - - +
159A ILE* 1.3 67.5 + - + +
161A LEU 3.3 0.3 + - - -
162A TRP* 3.0 58.5 + - + +
198A LEU* 3.7 26.1 - - + +
201A GLU* 5.4 4.2 + - - -
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Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A CYS* 4.2 19.1 - - - -
124A GLN* 3.7 45.8 - - + +
127A LEU* 3.6 25.4 - - + -
128A PHE* 3.6 21.8 - - + -
155A PRO 3.3 17.1 + - - +
156A LEU* 3.7 9.4 - - + +
157A ALA 3.4 0.2 - - - -
158A LYS* 1.3 79.2 - - + +
160A ILE* 1.3 61.5 + - - +
162A TRP* 4.1 2.7 - - - +
163A SER* 3.5 20.4 + - - -
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Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 4.3 25.6 - - + +
128A PHE* 4.5 9.0 - - + -
131A LEU* 4.7 9.9 - - + -
147A LEU* 3.2 37.7 - - + -
151A ILE* 3.7 15.9 - - + -
156A LEU 3.3 8.9 + - - +
157A ALA 3.9 6.1 - - - +
159A ILE* 1.3 77.3 - - - +
161A LEU* 1.3 62.7 + - - +
163A SER* 2.6 24.7 + - - +
166A PHE* 3.3 12.8 - - + +
169A PHE* 4.2 13.0 - - + -
191A LEU* 3.8 25.6 - - + -
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ALA* 3.0 20.3 + - + +
158A LYS 3.3 0.2 + - - -
160A ILE* 1.3 77.2 - - - +
162A TRP* 1.3 74.4 + - + +
163A SER 3.3 2.9 + - - +
166A PHE* 3.4 40.7 - - + +
167A TYR* 5.1 0.5 + - - -
191A LEU* 3.6 40.2 - - + +
192A LEU* 5.0 2.5 - - + -
198A LEU* 4.0 26.2 - - + +
199A SER* 4.9 3.4 - - - -
202A PHE* 3.1 51.2 - - + -
206A HIS* 4.5 1.6 + - - -
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Residues in contact with TRP 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LYS* 3.0 46.8 + - + +
159A ILE* 4.1 3.8 - - - +
161A LEU* 1.3 83.3 - - + +
163A SER* 1.3 60.2 + - - +
198A LEU* 3.5 39.7 - - + -
201A GLU* 4.0 8.3 - - + -
202A PHE* 3.5 33.9 - - + -
205A GLN* 3.1 38.5 + - - -
206A HIS* 3.4 27.6 + + - -
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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