Contacts of the helix formed by residues 174 - 186 (chain B) in PDB entry 1N1E
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 ASP 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B SER* 3.6 6.1 + - - -
173B ALA* 1.3 78.2 - - + +
175B ILE* 1.3 65.3 + - - +
176B ASN* 3.0 31.0 + - - +
177B VAL* 3.0 36.6 + - + +
178B ALA 3.3 7.8 + - - -
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Residues in contact with ILE 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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349A ASP* 4.1 10.1 - - - +
173B ALA 3.9 3.6 + - - -
174B ASP* 1.3 74.5 + - - +
176B ASN* 1.3 66.7 + - - +
178B ALA* 3.3 4.3 + - + +
179B ARG* 2.9 62.0 + - - +
196B ALA* 3.8 24.9 - - + +
197B THR* 3.8 25.6 - - - +
198B THR* 3.8 16.6 - - + +
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Residues in contact with ASN 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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174B ASP* 3.0 19.8 + - - +
175B ILE* 1.3 79.9 - - - +
177B VAL* 1.3 60.8 + - + +
179B ARG* 3.6 28.5 + - - +
180B ARG* 3.1 26.7 + - - +
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Residues in contact with VAL 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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119B PRO* 5.9 4.0 - - + -
146B PRO 5.3 12.1 - - - +
147B LEU 6.1 1.1 - - - +
149B SER* 3.6 11.2 - - - +
172B SER* 3.4 19.5 - - - +
174B ASP* 3.0 30.2 + - + +
176B ASN* 1.3 76.5 - - + +
178B ALA* 1.3 64.9 + - - +
180B ARG* 3.2 7.1 + - - +
181B LEU* 3.0 31.2 + - + +
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Residues in contact with ALA 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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170B ILE* 3.6 34.5 - - - +
172B SER* 3.7 13.8 - - - -
174B ASP 3.3 3.0 + - - +
175B ILE* 3.3 12.5 + - - +
177B VAL* 1.3 79.3 - - - +
179B ARG* 1.3 57.1 + - - +
181B LEU* 3.4 2.9 + - - +
182B GLN* 2.9 29.1 + - - +
196B ALA* 3.8 11.2 - - + +
197B THR 3.8 13.9 - - - +
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Residues in contact with ARG 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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349A ASP* 2.9 35.2 + - - +
175B ILE* 2.9 36.9 + - - +
176B ASN* 3.6 26.3 + - - +
177B VAL 3.2 0.2 - - - -
178B ALA* 1.3 72.7 - - - +
180B ARG* 1.3 65.3 + - - +
182B GLN* 3.4 22.0 + - - +
183B ARG* 3.2 29.7 + - - +
196B ALA* 4.0 8.1 - - + -
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Residues in contact with ARG 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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13B LEU* 3.8 31.4 - - + +
15B LEU* 5.3 8.1 - - - +
119B PRO* 5.7 7.7 - - - +
176B ASN 3.1 15.1 + - - +
177B VAL* 3.2 11.0 + - + +
179B ARG* 1.3 77.4 - - - +
181B LEU* 1.3 60.7 + - + +
183B ARG* 3.0 33.7 + - - +
184B ILE* 3.1 27.3 + - + +
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Residues in contact with LEU 181 (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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88B ILE* 4.0 20.4 - - + -
119B PRO* 3.9 28.0 - - + -
120B VAL 5.0 3.8 - - - +
121B LEU* 4.2 10.1 - - + -
149B SER* 3.3 38.1 - - - +
170B ILE* 3.9 21.3 - - + -
177B VAL* 3.0 25.5 + - + +
178B ALA 3.7 3.8 - - - +
180B ARG* 1.3 78.5 - - + +
182B GLN* 1.3 57.6 + - - +
184B ILE* 3.1 13.0 + - + +
185B MET* 2.9 36.1 + - + +
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Residues in contact with GLN 182 (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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347A LEU* 3.8 22.8 - - + +
348A GLN* 2.7 36.4 + - - +
9B LYS 5.8 0.2 - - - +
170B ILE* 4.0 4.7 - - + +
178B ALA 2.9 16.2 + - - +
179B ARG* 3.5 26.4 - - - +
180B ARG 3.2 0.2 - - - -
181B LEU* 1.3 76.0 - - - +
183B ARG* 1.3 58.1 + - + +
186B SER* 2.7 36.4 + - - -
194B CYS* 2.7 46.4 + - + +
195B TRP* 3.6 1.8 - - - +
196B ALA* 3.8 12.2 - - + +
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Residues in contact with ARG 183 (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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347A LEU* 4.1 15.3 - - + -
9B LYS* 3.5 57.0 - - - +
11B GLU* 2.9 34.3 + - - +
12B LEU* 3.6 6.4 + - - +
13B LEU* 2.9 50.0 + - + +
37B LYS* 2.9 18.4 + - - -
179B ARG* 3.2 19.9 + - - +
180B ARG* 3.0 16.7 + - - +
182B GLN* 1.3 77.9 - - + +
184B ILE* 1.3 58.1 + - - +
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Residues in contact with ILE 184 (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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13B LEU* 3.8 21.5 - - + +
15B LEU* 3.7 42.0 - - + -
34B LEU* 4.5 10.1 - - + +
37B LYS* 2.6 36.2 + - + +
87B GLU 5.6 1.6 - - - +
88B ILE* 4.2 17.9 - - + -
119B PRO* 5.6 5.2 - - + -
180B ARG* 3.1 31.2 + - - +
181B LEU* 3.1 26.9 + - + +
183B ARG* 1.3 77.5 - - - +
185B MET* 1.3 58.7 + - - +
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Residues in contact with MET 185 (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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30B LEU* 4.4 22.9 - - + +
33B VAL* 3.4 25.6 - - + +
34B LEU* 3.6 35.9 - - + -
37B LYS* 4.5 1.2 - - - +
88B ILE* 4.4 12.1 - - + -
90B LEU* 4.4 6.3 - - + -
121B LEU* 4.0 31.2 - - + -
151B LEU* 4.5 2.2 - - + -
170B ILE* 4.0 5.8 - - + -
181B LEU* 2.9 19.4 + - - +
184B ILE* 1.3 78.1 - - + +
186B SER* 1.3 64.0 + - - +
187B THR* 3.8 1.6 + - - +
192B PHE* 3.4 22.1 - - + -
194B CYS* 3.6 19.1 - - - -
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Residues in contact with SER 186 (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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347A LEU* 3.5 21.1 - - - +
12B LEU* 3.8 14.8 - - - +
37B LYS* 2.8 26.0 + - - -
182B GLN 2.7 22.2 + - - -
184B ILE 3.5 0.2 - - - -
185B MET* 1.3 77.3 - - - +
187B THR* 1.3 62.6 + - - +
190B ARG* 5.5 2.0 - - - -
192B PHE 3.2 11.7 - - - -
193B VAL* 4.5 0.4 - - - -
194B CYS* 3.0 28.0 + - - +
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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