Contacts of the helix formed by residues 124 - 133 (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 GLN 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ILE* 3.4 11.9 - - - +
121A CYS* 3.1 27.8 + - - +
122A THR 3.8 1.4 + - - -
123A GLN* 1.3 71.2 - - - +
125A ASN* 1.3 62.1 + - - +
126A ILE 3.1 6.1 - - - -
127A LEU* 3.1 23.6 + - - +
128A PHE* 3.4 18.9 - - + -
159A ILE* 3.7 41.0 - - + +
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Residues in contact with ASN 125 (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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123A GLN* 3.4 5.0 - - + +
124A GLN* 1.3 74.1 - - - +
126A ILE* 1.3 56.0 + - - +
128A PHE* 3.1 21.9 + - - +
129A MET* 2.8 64.7 + - + +
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Residues in contact with ILE 126 (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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80A LEU* 4.3 5.4 - - + +
81A SER* 3.9 36.8 - - - +
84A VAL* 4.0 6.8 - - + +
102A PHE* 3.8 29.8 - - + -
119A TYR* 4.2 13.2 - - + -
120A ILE* 4.4 17.9 - - + -
123A GLN* 3.4 35.8 + - + +
125A ASN* 1.3 77.3 - - - +
127A LEU* 1.3 58.4 + - + +
129A MET* 3.3 12.6 + - + +
130A LEU* 3.0 37.1 + - + +
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Residues in contact with LEU 127 (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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120A ILE* 3.9 18.6 - - + -
124A GLN* 3.1 11.1 + - - +
126A ILE* 1.3 76.6 - - + +
128A PHE* 1.3 63.2 + - + +
130A LEU* 3.4 7.8 + - + +
131A LEU* 3.1 27.5 + - - +
147A LEU* 4.6 6.0 - - + +
150A CYS* 3.8 36.6 - - + -
156A LEU* 3.9 33.0 - - + +
159A ILE* 3.6 32.1 - - + -
160A ILE* 4.3 20.5 - - + +
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Residues in contact with PHE 128 (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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124A GLN* 3.4 31.6 - - + -
125A ASN* 3.1 22.9 + - - +
127A LEU* 1.3 76.1 - - + +
129A MET* 1.3 59.3 + - - +
131A LEU* 3.5 8.7 + - + +
132A LYS* 2.9 29.6 + - - +
159A ILE* 3.6 30.1 - - + -
160A ILE* 4.5 9.9 - - + -
163A SER* 3.5 35.2 - - - -
165A GLN* 3.9 38.5 - - + +
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Residues in contact with MET 129 (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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81A SER* 3.8 30.7 - - - +
84A VAL* 3.8 18.8 - - + +
85A ALA* 3.5 25.8 - - + -
125A ASN* 2.8 46.4 + - + +
126A ILE* 3.6 19.1 - - + +
128A PHE* 1.3 71.0 - - - +
130A LEU* 1.3 59.0 + - - +
132A LYS* 3.5 8.1 + - - +
133A GLY* 3.0 23.9 + - - -
139A ILE* 5.6 0.5 - - - +
143A CYS* 4.5 2.3 - - - -
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Residues in contact with LEU 130 (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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84A VAL* 3.8 21.3 - - + -
102A PHE* 4.5 2.9 - - + -
126A ILE* 3.0 31.9 + - + +
127A LEU* 3.6 9.2 - - - +
129A MET* 1.3 73.6 - - - +
131A LEU* 1.3 64.4 + - - +
133A GLY* 3.1 9.5 + - - -
134A TYR* 4.0 4.2 + - - -
143A CYS* 3.3 31.8 - - - +
146A MET* 3.8 38.4 - - + -
147A LEU* 4.0 32.5 - - + +
150A CYS* 4.0 20.9 - - - -
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Residues in contact with LEU 131 (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 3.1 16.4 + - - +
128A PHE* 3.7 10.8 - - + +
130A LEU* 1.3 76.1 - - - +
132A LYS* 1.3 61.3 + - - +
133A GLY 3.1 1.0 + - - -
134A TYR* 3.2 26.0 + - + +
147A LEU* 4.3 14.9 - - + +
160A ILE* 4.7 11.4 - - + -
165A GLN* 3.6 42.2 - - + +
166A PHE* 4.3 2.7 - - - +
168A ASP* 5.3 0.9 - - + +
169A PHE* 3.8 33.9 - - + -
172A TYR* 3.5 28.6 - - + +
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Residues in contact with LYS 132 (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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128A PHE 2.9 18.1 + - - +
129A MET* 3.8 8.1 - - - +
130A LEU 3.3 0.2 - - - -
131A LEU* 1.3 74.9 - - - +
133A GLY* 1.3 61.3 + - - +
134A TYR 3.1 1.5 + - - -
135A GLU* 3.2 52.9 + - + +
136A SER* 4.4 3.3 + - - -
165A GLN* 6.2 1.0 - - - +
168A ASP* 3.9 16.2 + - - +
171A ARG* 4.5 3.6 - - - +
172A TYR* 3.8 5.4 - - - +
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Residues in contact with GLY 133 (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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129A MET 3.0 10.7 + - - -
130A LEU 3.1 8.7 + - - -
131A LEU 3.1 2.2 - - - -
132A LYS* 1.3 76.0 - - - +
134A TYR* 1.3 61.9 + - - +
135A GLU 3.1 0.2 - - - -
136A SER 3.1 22.5 + - - +
139A ILE* 3.7 14.9 - - - +
140A ALA* 3.3 12.2 + - - -
143A CYS* 3.8 17.9 - - - -
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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