Contacts of the helix formed by residues 118 - 129 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B PRO 4.0 1.2 + - - -
117B TYR* 1.3 79.6 - - - +
119B PHE* 1.3 64.4 + - - +
120B SER* 3.3 21.6 + - - -
121B CYS* 3.1 21.4 + - - +
122B LEU* 3.2 13.2 + - - +
13D G 3.8 24.2 + - - -
14D C 3.5 11.0 - - - -
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Residues in contact with PHE 119 (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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118B SER* 1.3 73.6 - - - +
120B SER* 1.3 60.3 + - - +
122B LEU* 3.6 17.4 - - + +
123B ILE* 3.1 29.3 + - - +
144B ILE* 4.9 2.5 - - + -
151B PHE* 3.6 40.8 - + - -
158B TRP* 4.1 14.6 - + + -
161B SER* 3.5 34.3 - - - -
162B VAL* 3.6 28.0 - - + -
165B ASN* 3.7 10.3 - - + +
14D C 2.6 40.9 + - - +
15D T 4.2 7.4 - - - -
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Residues in contact with SER 120 (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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118B SER* 3.1 10.0 + - - -
119B PHE* 1.3 78.8 - - - +
121B CYS* 1.3 58.7 + - - +
124B PHE* 3.1 25.8 + - - +
165B ASN* 2.6 34.6 + - - +
169B ASN* 3.9 8.0 + - - -
172B PHE* 3.3 11.7 - - - -
199B LEU* 4.3 12.0 - - - +
13D G 2.5 30.7 + - - -
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Residues in contact with CYS 121 (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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117B TYR* 3.6 25.4 - - + -
118B SER* 3.1 13.1 + - - +
120B SER* 1.3 79.9 - - - +
122B LEU* 1.3 60.0 + - - +
124B PHE* 3.6 6.8 - - - +
125B MET* 3.0 36.0 + - - +
199B LEU* 4.7 4.9 - - - -
202B ALA* 3.9 29.6 - - - -
203B LEU* 3.8 31.9 - - + -
206B THR* 5.5 1.6 - - - -
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Residues in contact with LEU 122 (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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115B PRO* 4.5 6.1 - - + -
117B TYR* 3.7 25.1 - - + +
118B SER 3.2 13.2 + - - +
119B PHE* 3.6 34.8 - - + +
120B SER 3.4 0.2 - - - -
121B CYS* 1.3 74.1 - - - +
123B ILE* 1.3 64.7 + - - +
125B MET* 3.5 21.6 + - + -
126B ALA* 3.1 23.2 + - - +
143B TRP* 3.7 7.8 - - + -
144B ILE* 4.1 22.6 - - + +
148B PHE* 3.7 17.7 - - + -
151B PHE* 3.9 22.2 - - + -
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Residues in contact with ILE 123 (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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119B PHE 3.1 19.5 + - - +
122B LEU* 1.3 75.3 - - - +
124B PHE* 1.3 64.1 + - - +
126B ALA* 3.3 0.9 + - - +
127B ILE* 3.1 37.1 + - + +
140B ILE* 4.0 28.3 - - + -
144B ILE* 5.0 3.1 - - + -
162B VAL* 3.4 40.6 - - + +
165B ASN* 4.2 8.1 - - + -
166B LEU* 3.9 26.0 - - + +
172B PHE* 3.6 26.2 - - + -
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Residues in contact with PHE 124 (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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120B SER 3.1 20.8 + - - +
121B CYS* 3.6 6.7 - - - +
122B LEU 3.2 0.2 - - - -
123B ILE* 1.3 76.9 - - - +
125B MET* 1.3 62.9 + - + +
127B ILE* 4.1 1.2 - - - +
128B GLU* 3.1 56.6 + - + +
172B PHE* 4.1 6.7 - - - -
191B ILE* 4.0 18.2 - - + -
196B ARG* 4.8 1.8 - - + -
199B LEU* 3.6 45.1 - - + -
200B ILE* 3.6 38.6 - - + -
203B LEU* 4.2 25.8 - - + -
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Residues in contact with MET 125 (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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117B TYR* 4.1 19.5 - - + -
121B CYS 3.0 24.1 + - - +
122B LEU* 3.6 28.9 - - + +
124B PHE* 1.3 78.8 - - + +
126B ALA* 1.3 65.5 + - - +
128B GLU* 3.5 4.3 + - - -
129B ASP* 3.1 30.7 + - - +
143B TRP* 3.5 24.9 - - + -
148B PHE* 4.4 3.6 - - + -
203B LEU* 3.7 33.2 - - + -
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Residues in contact with ALA 126 (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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122B LEU 3.1 18.1 + - - +
123B ILE* 3.8 7.0 - - - +
124B PHE 3.3 0.2 - - - -
125B MET* 1.3 77.3 - - - +
127B ILE* 1.3 61.3 + - - +
129B ASP* 3.4 11.3 + - - +
130B SER 3.5 5.0 + - - -
135B LEU* 3.3 22.0 - - + +
140B ILE* 4.5 14.4 - - + -
143B TRP* 3.6 42.0 - - + -
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Residues in contact with ILE 127 (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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123B ILE* 3.1 32.3 + - + +
124B PHE 4.1 0.2 - - - +
126B ALA* 1.3 76.0 - - - +
128B GLU* 1.3 61.8 + - - +
130B SER* 2.4 28.4 + - - -
133B LYS* 3.3 32.8 - - + +
134B ARG* 3.8 5.8 - - - +
135B LEU* 4.2 10.8 - - + -
140B ILE* 4.5 11.0 - - + -
172B PHE* 4.3 4.0 - - + -
189B TRP* 4.1 22.7 - - + +
190B CYS* 4.2 9.0 - - - -
191B ILE* 3.8 35.7 - - + -
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Residues in contact with GLU 128 (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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124B PHE* 3.1 46.5 + - + +
125B MET* 4.0 6.1 - - - +
127B ILE* 1.3 75.7 - - - +
129B ASP* 1.3 64.9 + - - +
130B SER 3.6 1.4 + - - +
133B LYS* 2.9 52.9 + - - +
191B ILE* 4.1 14.9 - - + +
196B ARG* 3.1 35.3 + - - -
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Residues in contact with ASP 129 (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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125B MET* 3.1 18.4 + - - +
126B ALA 3.8 3.6 - - - +
127B ILE 3.2 0.4 - - - -
128B GLU* 1.3 80.8 - - - +
130B SER* 1.3 62.3 + - - +
131B PRO* 4.0 1.2 - - - +
143B TRP* 3.2 37.5 + - + +
147B HIS* 4.6 4.5 + - - -
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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