Contacts of the helix formed by residues 280 - 288 (chain B) in PDB entry 1N8T
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 GLY 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B MET* 4.1 4.7 - - - -
275B LEU* 3.2 21.8 + - - -
277B SER 2.7 10.9 + - - -
279B ILE* 1.3 76.8 - - - +
281B LEU* 1.3 53.6 + - - +
282B SER 3.2 2.9 - - - -
283B ILE* 2.6 47.3 + - - +
284B ALA 3.0 4.0 + - - -
292B PHE* 4.0 6.5 - - - -
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B MET* 3.5 47.0 - - + +
131B PHE* 3.9 32.3 - - + -
132B CYS* 4.9 2.7 - - + -
206B ILE* 4.0 16.4 - - + -
243B VAL* 4.3 4.0 - - + -
245B LEU* 3.9 24.5 - - + -
263B PHE* 4.3 11.2 - - + -
278B ALA 3.1 17.5 + - - +
279B ILE 3.2 1.2 - - - -
280B GLY* 1.3 74.9 - - - +
282B SER* 1.3 59.8 + - - +
284B ALA* 3.1 6.0 + - + +
285B LEU* 2.8 36.1 + - + +
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 4.3 3.1 - - - -
153B ASN* 3.8 16.9 + - - -
163B PRO* 3.4 25.1 - - - +
167B THR* 4.0 1.9 - - - +
180B VAL* 3.7 19.7 - - - +
182B PHE* 3.7 9.3 - - - -
206B ILE* 4.0 22.1 - - - +
245B LEU* 5.7 0.4 - - - +
279B ILE 4.5 1.7 + - - -
280B GLY 3.2 0.4 - - - -
281B LEU* 1.3 77.8 - - - +
283B ILE* 1.3 61.8 + - - +
285B LEU* 3.8 5.2 - - - -
286B HIS* 3.1 24.6 + - - +
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B PRO* 3.8 30.1 - - + -
166B VAL* 3.7 33.0 - - + -
167B THR* 3.8 14.4 - - + -
170B LEU* 4.9 2.2 - - + -
275B LEU* 4.0 20.9 - - + +
280B GLY* 2.6 33.4 + - - +
282B SER* 1.3 70.7 + - - +
284B ALA* 1.3 59.6 + - - +
286B HIS* 3.2 2.6 + - - +
287B VAL* 3.0 46.1 + - + +
292B PHE* 4.0 18.6 - - + -
295B LEU* 4.4 3.6 - - + -
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Residues in contact with ALA 284 (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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128B MET* 5.0 0.2 - - + -
132B CYS* 3.6 10.8 - - + -
280B GLY 3.0 6.0 + - - +
281B LEU* 3.5 13.9 - - + +
283B ILE* 1.3 78.0 - - - +
285B LEU* 1.3 58.8 + - - +
288B GLY* 2.7 41.2 + - - -
289B PHE* 3.8 31.6 - - + -
292B PHE* 4.1 17.4 - - + -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE* 4.2 9.0 - - + -
132B CYS* 3.8 26.7 - - + +
135B VAL* 3.6 36.6 - - + -
136B ARG* 2.9 26.8 + - + +
151B VAL* 4.0 23.6 - - + -
178B PRO* 3.3 15.9 - - + +
180B VAL* 5.6 0.7 - - + -
204B LEU* 4.7 1.8 - - + -
206B ILE* 3.9 19.5 - - + -
281B LEU* 2.8 40.4 + - + +
282B SER* 4.0 4.9 - - - +
284B ALA* 1.3 76.4 - - - +
286B HIS* 1.3 58.1 + - - +
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Residues in contact with HIS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ARG* 3.1 11.7 + - - -
167B THR* 3.9 19.3 + - + +
171B LYS* 3.2 40.9 + - + -
174B SER* 3.3 46.8 + - - +
177B GLY* 3.8 2.1 - - - -
178B PRO* 2.9 32.1 + - - -
179B ARG* 4.5 3.4 - - - -
180B VAL* 3.6 26.8 + - + +
282B SER 3.1 19.6 + - - +
283B ILE 3.2 3.1 + - - +
285B LEU* 1.3 78.6 - - - +
287B VAL* 1.3 62.3 + - + +
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ARG* 3.5 8.0 + - - +
167B THR* 5.6 2.2 - - + +
170B LEU* 3.6 30.1 - - + +
173B TYR* 3.2 33.4 - - + +
174B SER* 4.0 4.5 - - - -
283B ILE* 3.0 33.7 + - + +
286B HIS* 1.3 87.9 - - + +
288B GLY* 1.3 65.4 + - - +
291B ASN* 3.0 39.5 - - + +
292B PHE 4.5 3.1 - - - +
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B CYS* 4.6 0.2 - - - -
136B ARG* 3.5 25.3 - - - +
284B ALA 2.7 25.6 + - - +
287B VAL* 1.3 77.5 - - - +
289B PHE* 1.3 61.8 + - - -
290B ASP 3.3 2.7 - - - -
291B ASN 3.5 0.4 + - - -
292B PHE* 3.1 23.2 + - - +
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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
------------------------------------------------------------
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