Contacts of the helix formed by residues 170 - 180 (chain B) in PDB entry 1N34
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 GLU 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B VAL* 3.2 34.1 - - + -
73B THR* 3.6 14.8 + - - +
97B TRP* 3.1 45.4 + - + +
164B VAL* 4.5 7.8 - - + +
165B VAL* 6.3 0.2 - - + -
166B ASP 3.1 7.7 + - - +
167B PRO* 3.0 13.9 - - - +
169B LYS* 1.3 98.7 + - + +
171B ALA* 1.3 58.8 + - - +
172B ILE* 3.6 10.0 + - - +
173B ALA* 3.4 17.1 + - + +
174B VAL* 3.7 8.1 - - - +
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Residues in contact with ALA 171 (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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167B PRO 3.0 18.4 - - - +
168B THR* 4.1 7.6 - - - +
169B LYS 2.5 10.3 + - - +
170B GLU* 1.3 72.7 - - - +
172B ILE* 1.3 68.4 + - + +
173B ALA 3.1 1.6 - - - -
174B VAL* 3.7 10.5 - - + +
175B ARG* 3.0 33.7 + - + +
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Residues in contact with ILE 172 (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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1101A A 3.1 54.1 - - + +
97B TRP* 3.4 21.1 - - + +
98B LEU 5.0 2.0 - - - +
99B GLY* 5.3 0.4 - - - -
169B LYS 5.1 2.5 - - - +
170B GLU* 3.6 9.6 + - - +
171B ALA* 1.3 87.3 - - + +
173B ALA* 1.3 71.4 + - - +
175B ARG* 3.6 14.8 - - - +
176B GLU* 2.8 24.5 + - + +
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Residues in contact with ALA 173 (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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71B VAL* 4.3 10.5 - - + -
97B TRP* 3.3 35.0 - - + +
162B ILE* 5.0 9.6 - - + -
164B VAL* 5.7 2.2 - - + -
170B GLU* 3.4 27.4 + - + +
172B ILE* 1.3 74.4 - - - +
174B VAL* 1.3 59.6 + - + +
176B GLU* 2.4 35.9 + - - +
177B ALA* 3.1 6.3 + - - -
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Residues in contact with VAL 174 (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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162B ILE* 5.6 1.4 - - - +
164B VAL* 4.7 13.0 - - + -
167B PRO* 3.8 25.8 - - + -
170B GLU 3.7 17.9 - - - +
171B ALA* 3.7 11.2 - - + +
173B ALA* 1.3 77.0 - - - +
175B ARG* 1.3 66.1 + - - +
177B ALA* 2.8 18.8 + - - +
178B ARG* 3.1 14.8 + - - -
184B VAL* 4.9 13.0 - - + -
196B LEU* 3.5 44.2 - - + +
197B VAL* 5.9 3.4 - - + -
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Residues in contact with ARG 175 (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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1075A C 3.8 26.2 + - - -
1076A C 4.4 8.3 + - - -
1101A A 4.3 20.4 + - - +
171B ALA* 3.0 24.3 + - + +
172B ILE* 3.6 13.6 - - - +
173B ALA 2.8 2.2 + - - -
174B VAL* 1.3 81.4 - - + +
176B GLU* 1.3 64.8 + - - +
177B ALA 3.3 0.2 + - - -
178B ARG* 3.4 16.3 + - - +
179B LYS* 3.6 38.4 + - - +
196B LEU* 5.7 7.6 - - + -
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Residues in contact with GLU 176 (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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1101A A 3.3 17.4 + - - +
97B TRP* 2.9 26.7 - - + -
100B GLY* 2.8 27.9 + - - -
102B LEU* 3.0 14.0 + - + -
103B THR* 2.4 54.8 + - - +
172B ILE* 2.8 18.1 + - + +
173B ALA 2.4 24.2 + - - +
175B ARG* 1.3 70.4 - - + +
177B ALA* 1.3 48.5 + - - +
179B LYS* 2.4 40.5 + - - +
180B LEU* 4.5 2.4 - - - +
182B ILE* 5.2 0.2 - - - -
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Residues in contact with ALA 177 (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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102B LEU* 4.7 3.7 - - - +
162B ILE* 4.7 11.4 - - + -
173B ALA 3.1 4.7 + - - +
174B VAL* 2.8 14.1 + - - +
176B GLU* 1.3 66.6 - - - +
178B ARG* 1.3 56.0 + - - +
179B LYS 2.4 29.6 + - - +
182B ILE* 3.2 40.1 + - + +
184B VAL* 3.2 33.2 - - + -
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Residues in contact with ARG 178 (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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174B VAL* 3.1 12.4 + - - +
175B ARG* 3.6 12.6 - - - +
177B ALA* 1.3 78.4 - - - +
179B LYS* 1.3 56.4 + - - +
180B LEU 3.9 1.8 + - - -
181B PHE* 3.9 6.0 + - - +
184B VAL* 4.9 6.6 - - - +
195B ASP 3.5 4.8 + - - -
196B LEU* 2.9 56.5 + - + +
197B VAL* 3.5 2.6 - - - +
198B ASP* 4.1 14.4 + - - +
68H ARG* 2.5 34.4 - - - +
69H ARG 4.7 1.2 + - - -
70H GLN* 5.2 2.6 + - - +
71H GLY* 2.9 37.3 + - - +
72H PRO* 2.8 45.2 - - + +
74H PRO* 4.4 10.8 - - - +
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Residues in contact with LYS 179 (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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1075A C 3.1 31.1 + - - +
1076A C 2.6 40.2 + - - -
103B THR* 5.2 4.7 - - + +
175B ARG* 3.8 25.7 - - - +
176B GLU* 2.4 30.6 + - - +
177B ALA 2.4 13.6 + - - +
178B ARG* 1.3 75.8 - - - +
180B LEU* 1.3 70.6 + - + +
181B PHE* 5.7 0.4 - - - -
182B ILE* 3.4 1.2 - - - +
72H PRO* 4.3 22.2 - - + -
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Residues in contact with LEU 180 (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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102B LEU* 4.5 8.1 - - + +
103B THR* 4.0 35.0 - - + +
158B LEU* 4.9 10.6 - - + +
176B GLU 4.5 2.5 - - - +
179B LYS* 1.3 79.9 - - + +
181B PHE* 1.3 85.8 + - - +
182B ILE* 2.7 27.6 - - + +
64E ARG* 4.7 16.6 - - - +
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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