Contacts of the helix formed by residues 118 - 126 (chain M) in PDB entry 6N1H
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 118 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114M PHE* 3.3 52.4 + + - +
115M ILE 4.0 3.6 - - - -
117M GLN* 1.3 100.1 + - + +
119M ARG* 1.3 56.4 + - - +
120M ALA 3.3 2.9 - - - -
121M ALA* 3.2 8.6 + - + +
122M LEU* 2.9 31.7 + - + +
192M LEU* 3.3 53.9 + - + +
193M GLU* 5.2 0.6 - - - -
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Residues in contact with ARG 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J ASP* 3.8 9.2 + - - -
137J TYR* 3.2 55.3 + - + -
143J ASP* 5.5 1.2 + - - -
146J TYR* 3.3 37.6 + - - -
115M ILE 3.8 9.4 + - - +
116M ASP* 3.9 15.9 - - - +
117M GLN 3.4 4.4 + - - -
118M HIS* 1.3 77.6 - - - +
120M ALA* 1.3 62.0 + - - +
123M ILE* 3.2 49.7 + - - +
160M ARG* 4.6 6.3 + - - +
163M PHE* 3.7 52.8 + - + +
164M SER* 5.7 0.6 - - - +
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Residues in contact with ALA 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J TRP* 5.2 10.5 + - + +
134J ASP* 3.8 37.9 + - + +
135J ALA* 4.7 4.5 - - - +
117M GLN 5.2 0.2 + - - -
118M HIS 3.3 0.6 - - - -
119M ARG* 1.3 79.8 - - - +
121M ALA* 1.3 60.4 + - - +
123M ILE* 3.9 2.9 + - - +
124M ALA* 3.6 20.8 + - - +
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Residues in contact with ALA 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118M HIS* 3.2 16.1 + - + +
120M ALA* 1.3 79.2 - - - +
122M LEU* 1.3 60.7 + - - +
123M ILE 3.2 0.7 - - - -
124M ALA* 4.7 2.0 - - - +
125M ARG* 3.0 42.9 + - - +
188M LEU* 5.4 0.7 - - - +
192M LEU* 4.2 28.7 - - + -
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Residues in contact with LEU 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M PHE* 4.4 8.5 - - + +
115M ILE* 4.1 35.0 - - + +
118M HIS* 2.9 20.6 + - + +
121M ALA* 1.3 74.1 - - - +
123M ILE* 1.3 64.3 + - - +
125M ARG 4.3 0.2 - - - -
126M VAL* 3.2 42.7 - - + +
159M MET* 3.3 12.0 - - + +
163M PHE* 3.7 27.6 - - + -
177M LEU* 5.6 0.7 - - + -
181M LEU* 4.0 17.7 - - + -
188M LEU* 4.3 10.1 - - + -
189M VAL* 6.1 0.9 - - + -
192M LEU* 3.9 22.0 - - + -
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Residues in contact with ILE 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J TRP* 6.2 0.7 - - + -
134J ASP* 3.3 30.5 - - - +
119M ARG* 3.2 37.7 + - - +
120M ALA 4.2 4.7 - - - +
121M ALA 3.2 0.4 - - - -
122M LEU* 1.3 81.7 - - - +
124M ALA* 1.3 64.3 + - + +
125M ARG 3.4 0.7 + - - -
126M VAL 4.2 4.0 + - - +
156M PRO* 3.3 42.5 - - + +
159M MET* 3.8 10.4 - - + +
160M ARG* 3.7 35.7 - - + +
163M PHE* 3.8 17.5 - - + -
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Residues in contact with ALA 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J TRP* 4.9 13.0 - - + +
120M ALA 3.6 13.9 + - - +
121M ALA* 3.5 2.7 + - - +
123M ILE* 1.3 81.2 - - + +
125M ARG* 1.3 70.0 + - + +
126M VAL 3.8 1.2 - - - +
127M THR* 5.3 3.3 - - - +
156M PRO* 4.4 14.5 - - - +
144N GLU* 4.4 13.2 - - - +
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Residues in contact with ARG 125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M ALA* 3.0 22.8 + - - +
124M ALA* 1.3 90.2 - - + +
126M VAL* 1.3 62.0 + - - +
127M THR* 3.7 10.9 + - - +
185M GLN* 4.8 2.8 + - - -
187M TYR* 6.2 1.4 - - - -
188M LEU* 3.3 39.5 - - + +
191M ASP* 3.7 23.1 + - - +
192M LEU* 3.3 31.5 - - - +
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Residues in contact with VAL 126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122M LEU* 3.2 38.8 + - + +
123M ILE 4.2 6.4 + - - +
124M ALA 3.8 1.2 - - - +
125M ARG* 1.3 75.1 - - - +
127M THR* 1.3 65.0 + - - +
128M ASN* 3.9 9.9 - - + +
129M VAL* 3.7 24.8 - - + +
132M LEU* 5.0 3.6 - - + -
155M ASN* 3.9 16.3 + - - +
156M PRO* 5.9 0.2 - - - +
159M MET* 3.9 16.8 - - + +
181M LEU* 4.2 18.4 - - + -
185M GLN* 5.3 3.6 - - - +
188M LEU* 3.7 21.8 - - + -
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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