Contacts of the helix formed by residues 165 - 169 (chain I) 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 PHE 165 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127E THR* 3.2 46.6 + - - +
130E GLU* 4.7 8.7 - - - -
155E ASN* 5.6 1.8 - - - -
141I LEU* 4.2 13.7 - - + -
145I GLN* 3.7 50.7 - - + +
148I ALA* 4.1 18.8 - - + -
149I VAL* 3.9 9.0 - - + -
161I LYS* 3.2 35.9 - - + -
162I LEU* 3.4 9.4 + - - +
163I PHE 3.2 0.4 - - - -
164I SER* 1.3 81.6 - - - +
166I THR* 1.3 61.8 - - - +
167I PRO 3.5 1.6 - - - -
168I ALA 3.5 2.8 + - - -
169I TRP* 3.2 28.1 + - + +
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Residues in contact with THR 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I ILE* 5.4 2.4 - - - +
116I ASP* 4.0 16.8 + - - -
162I LEU 3.7 3.8 + - - -
163I PHE* 3.2 32.9 + - - -
165I PHE* 1.3 74.2 - - - +
167I PRO* 1.4 70.3 - - - +
168I ALA 3.1 2.5 - - - -
169I TRP* 3.1 44.4 + - - +
174I LYS* 4.5 7.6 + - - +
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Residues in contact with PRO 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E ALA 3.9 17.0 - - - +
125E ARG* 2.7 40.1 + - + +
127E THR* 4.4 5.4 - - + -
137F TYR* 4.9 5.2 - - - +
143F ASP* 2.5 33.2 - - + +
147F GLN* 5.3 0.4 - - - +
163I PHE 3.4 14.1 - - - +
164I SER 3.9 8.1 - - - +
165I PHE 3.8 2.9 - - - -
166I THR* 1.4 90.4 - - - +
168I ALA* 1.3 56.3 + - - +
169I TRP 3.2 1.8 + - - +
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Residues in contact with ALA 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E ARG 2.6 23.7 + - - +
127E THR* 3.1 23.8 - - - +
185E GLN* 3.1 24.9 - - - +
187E TYR* 2.4 31.4 - - + +
188E LEU* 3.6 17.1 - - + +
165I PHE 3.5 4.1 + - - +
166I THR 3.1 1.6 - - - -
167I PRO* 1.3 77.2 - - - +
169I TRP* 1.3 52.4 + - - +
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Residues in contact with TRP 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E ARG* 2.8 18.1 + - - -
187E TYR* 2.7 32.2 + + - -
115I ILE* 5.6 5.2 - - + -
136I LEU* 4.8 5.6 - - + -
140I VAL* 2.7 32.6 - - + +
141I LEU* 4.4 15.3 - - + -
145I GLN* 5.2 0.2 + - - -
162I LEU* 4.3 22.4 - - + -
163I PHE* 6.3 0.4 - + - -
165I PHE* 3.2 22.2 + - + +
166I THR* 3.1 31.1 + - - +
167I PRO 4.1 1.0 - - - +
168I ALA* 1.3 80.8 - - - +
170I ASN* 1.3 60.0 + - - +
173I CYS* 3.6 13.7 - - - -
174I LYS* 3.7 36.6 + - + -
177I LEU* 3.6 38.6 - - + -
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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