Contacts of the helix formed by residues 118 - 129 (chain A) in PDB entry 6NCM
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 SER 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A TYR* 1.3 76.1 - - - +
119A PHE* 1.3 60.3 + - - +
120A SER* 3.8 8.5 + - - -
121A CYS* 3.0 23.7 + - - +
122A LEU* 2.8 27.1 + - - +
203A LEU* 5.3 3.5 - - - +
209A HIS* 3.8 24.7 + - - +
9D A 4.4 15.3 + - - -
10D G 3.2 20.4 - - - -
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Residues in contact with PHE 119 (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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114A LYS* 3.3 33.4 - - - -
117A TYR 3.9 0.2 + - - -
118A SER* 1.3 74.7 - - - +
120A SER* 1.3 58.0 + - - +
122A LEU* 3.3 20.6 + - + +
123A ILE* 3.0 37.5 + - + +
144A ILE* 6.0 0.2 - - + -
151A PHE* 4.6 9.4 - + - -
158A TRP* 3.7 32.8 - + + -
161A SER* 3.7 25.1 - - - +
162A VAL* 3.7 21.5 - - + -
165A ASN* 4.2 16.4 - - + +
10D G 3.4 26.4 + + + +
11D A 3.6 22.0 - - - -
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Residues in contact with SER 120 (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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118A SER* 3.2 8.7 + - - -
119A PHE* 1.3 78.8 - - - +
121A CYS* 1.3 57.0 + - - +
123A ILE 3.5 0.2 + - - -
124A PHE* 3.0 28.6 + - - +
165A ASN* 3.0 32.5 + - - +
169A ASN* 3.0 15.1 + - - -
172A PHE* 3.7 13.6 - - - -
199A LEU* 4.9 12.6 - - - +
203A LEU* 5.3 3.8 - - - -
9D A 4.1 14.2 + - - -
10D G 4.6 1.1 + - - -
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Residues in contact with CYS 121 (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 TYR* 4.0 15.3 - - + -
118A SER* 3.0 25.8 + - - +
120A SER* 1.3 77.0 - - - +
122A LEU* 1.3 59.9 + - - +
124A PHE* 3.3 0.5 + - - +
125A MET* 2.9 60.3 + - - +
203A LEU* 4.0 34.2 - - + +
207A PRO* 4.8 8.1 - - - +
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Residues in contact with LEU 122 (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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114A LYS* 5.3 1.6 - - - -
115A PRO* 5.8 1.8 - - + -
117A TYR* 3.7 29.2 - - + +
118A SER 2.8 19.0 + - - +
119A PHE* 3.7 23.6 - - + +
121A CYS* 1.3 78.0 - - - +
123A ILE* 1.3 61.1 + - - +
125A MET* 3.6 5.3 + - + -
126A ALA* 3.2 22.9 + - - +
143A TRP* 4.0 7.9 - - + -
144A ILE* 3.9 23.2 - - + +
148A PHE* 3.6 37.7 - - + -
151A PHE* 3.9 28.0 - - + -
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Residues in contact with ILE 123 (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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119A PHE 3.0 21.9 + - - +
120A SER 3.9 3.6 - - - +
122A LEU* 1.3 77.0 - - - +
124A PHE* 1.3 62.4 + - - +
126A ALA* 3.3 5.4 + - - +
127A ILE* 3.1 33.5 + - + +
140A ILE* 4.3 13.2 - - + -
144A ILE* 5.1 2.7 - - + -
162A VAL* 3.6 43.5 - - + +
165A ASN* 4.1 18.4 - - + +
166A LEU* 3.6 27.6 - - + -
172A PHE* 3.6 22.4 - - + -
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Residues in contact with PHE 124 (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 SER 3.0 18.8 + - - +
121A CYS 3.7 2.2 - - - +
123A ILE* 1.3 77.8 - - - +
125A MET* 1.3 71.6 + - + +
127A ILE* 3.5 0.7 + - - +
128A GLU* 3.1 58.4 + - + +
172A PHE* 4.5 5.8 - - + -
191A ILE* 3.5 24.7 - - + -
196A ARG* 4.5 11.7 - - + -
199A LEU* 3.7 25.8 - - + -
200A ILE* 3.4 33.7 - - + -
203A LEU* 3.7 25.6 - - + -
204A LYS* 5.3 5.4 - - - -
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Residues in contact with MET 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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117A TYR* 4.1 17.3 - - + -
121A CYS* 2.9 45.6 + - - +
122A LEU* 3.9 26.0 - - + +
124A PHE* 1.3 85.4 - - + +
126A ALA* 1.3 60.3 + - - +
128A GLU* 4.5 3.2 - - - +
129A ASP* 3.2 25.5 + - - +
143A TRP* 3.5 25.6 - - + -
148A PHE* 4.3 8.1 - - + -
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Residues in contact with ALA 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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122A LEU 3.2 18.2 + - - +
123A ILE 3.7 4.7 - - - +
124A PHE 3.2 0.4 - - - -
125A MET* 1.3 75.9 - - - +
127A ILE* 1.3 65.5 + - - +
129A ASP* 3.5 9.7 + - - +
130A SER* 3.6 5.4 + - - -
135A LEU* 3.3 21.2 - - + +
140A ILE* 4.5 16.8 - - + +
143A TRP* 3.5 39.9 - - + -
144A ILE* 4.9 0.2 - - + -
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Residues in contact with ILE 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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123A ILE* 3.1 34.7 + - + +
126A ALA* 1.3 76.1 - - - +
128A GLU* 1.3 64.0 + - - +
130A SER* 2.5 24.4 + - - -
133A LYS* 3.2 36.3 - - + +
134A ARG* 4.2 1.3 - - - +
135A LEU* 4.0 10.8 - - + -
140A ILE* 4.5 15.7 - - + -
172A PHE* 4.4 4.3 - - + -
189A TRP* 3.8 28.7 - - + +
190A CYS* 4.3 4.5 - - - +
191A ILE* 3.9 33.2 - - + -
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Residues in contact with GLU 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 PHE* 3.1 44.2 + - + +
125A MET* 4.5 3.6 - - - +
127A ILE* 1.3 75.7 - - - +
129A ASP* 1.3 59.3 + - - +
130A SER 3.2 5.6 + - - +
133A LYS* 3.2 46.4 + - - +
191A ILE* 3.7 12.5 - - + +
196A ARG* 2.9 41.4 + - - -
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Residues in contact with ASP 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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125A MET 3.2 19.2 + - - +
126A ALA 3.9 2.5 - - - +
127A ILE 3.2 1.0 - - - -
128A GLU* 1.3 77.1 - - - +
130A SER* 1.3 59.0 + - - +
131A PRO* 4.1 1.7 - - - +
143A TRP* 3.2 32.7 + - + +
147A HIS* 4.5 8.1 + - - -
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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