Contacts of the helix formed by residues 253 - 262 (chain B) in PDB entry 3O2M
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 GLN 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A GLU* 5.5 0.8 - - - +
185A GLU* 3.9 8.3 + - - -
198B LEU 5.3 2.1 + - - +
199B GLY 4.6 13.9 - - - +
252B LEU* 1.3 75.6 - - - +
254B PRO* 1.3 75.8 - - - +
255B THR* 3.3 3.5 + - - +
256B VAL* 3.0 20.6 + - + +
257B ARG* 2.7 30.1 + - - +
701B 46A 3.2 54.0 + - + -
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Residues in contact with PRO 254 (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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185A GLU* 3.5 27.8 - - + +
801A SO4 4.8 1.3 - - - -
252B LEU 3.7 3.1 - - - +
253B GLN* 1.3 98.9 - - + +
255B THR* 1.3 63.3 + - - +
257B ARG* 4.1 9.5 - - + +
258B ASN* 3.3 24.6 + - - +
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Residues in contact with THR 255 (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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184A PRO* 4.8 4.9 - - + -
185A GLU* 3.8 13.0 + - + +
230A TYR* 3.2 41.4 + - + +
701A 46A 3.7 23.5 - - + +
801A SO4 3.4 25.7 + - - +
253B GLN* 4.2 3.1 + - - +
254B PRO* 1.3 78.0 - - - +
256B VAL* 1.3 61.8 + - - +
258B ASN* 3.3 13.3 - - - +
259B TYR* 3.6 5.2 + - - +
701B 46A 3.6 24.6 - - - -
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A 46A 4.1 15.5 - - + -
198B LEU* 3.8 42.2 - - + +
252B LEU* 4.6 3.8 - - + -
253B GLN* 3.0 20.1 + - + +
255B THR* 1.3 74.3 - - - +
257B ARG* 1.3 66.3 + - - +
258B ASN 3.1 1.8 - - - -
259B TYR* 3.0 5.7 + - + +
260B VAL* 2.9 25.3 + - + +
701B 46A 3.5 46.2 - - + -
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Residues in contact with ARG 257 (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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246B PRO 5.5 0.2 + - - -
249B MET* 3.4 24.1 + - + +
250B LYS* 3.0 53.1 + - - +
252B LEU* 3.8 27.5 - - + +
253B GLN 2.7 19.4 + - - +
254B PRO* 4.1 8.7 - - - +
256B VAL* 1.3 72.1 - - - +
258B ASN* 1.3 63.9 + - - +
260B VAL* 3.3 1.0 + - - +
261B GLU* 3.0 64.1 + - + +
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Residues in contact with ASN 258 (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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189A ARG* 4.1 6.9 + - - +
228A ARG 3.9 17.0 + - - -
229A ASP* 4.2 9.0 - - + -
801A SO4 3.6 16.9 + - - +
254B PRO 3.3 11.4 + - - +
255B THR 3.3 14.4 - - - +
257B ARG* 1.3 83.3 - - - +
259B TYR* 1.3 62.3 + - - +
261B GLU* 3.4 9.9 + - - +
262B ASN* 3.3 24.6 + - - +
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Residues in contact with TYR 259 (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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229A ASP* 3.4 33.8 - - + +
231A ILE* 3.7 42.8 - - + +
232A ASP 5.4 0.4 - - - -
259A TYR* 5.1 2.3 + - - -
701A 46A 4.8 1.3 - - + -
231B ILE* 3.4 17.3 - - + +
234B TRP* 5.0 4.7 - + - -
235B ASN* 4.7 2.9 + - - -
255B THR 3.6 7.8 + - - +
256B VAL* 3.0 9.9 + - + +
258B ASN* 1.3 79.2 - - - +
260B VAL* 1.3 69.5 + - + +
262B ASN* 3.0 14.3 + - + +
263B ARG* 3.4 58.3 + - + -
701B 46A 3.8 29.8 - - + -
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Residues in contact with VAL 260 (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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198B LEU* 3.9 24.5 - - + -
234B TRP* 3.7 34.8 - - + +
243B THR* 5.7 1.6 - - + +
244B PRO* 5.5 0.4 - - + -
248B PHE* 6.0 0.2 - - + -
249B MET* 3.2 38.7 - - + +
252B LEU* 4.2 13.2 - - + -
256B VAL* 2.9 17.5 + - + +
257B ARG 3.8 3.1 - - - +
259B TYR* 1.3 82.4 - - + +
261B GLU* 1.3 61.9 + - - +
262B ASN 3.2 0.9 + - - -
263B ARG* 3.2 24.0 + - - +
265B LYS* 4.8 1.7 + - - -
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Residues in contact with GLU 261 (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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249B MET* 4.0 23.8 - - + +
257B ARG* 3.0 59.6 + - + +
258B ASN* 3.4 10.0 + - - +
260B VAL* 1.3 76.1 - - - +
262B ASN* 1.3 63.1 + - - +
263B ARG 3.3 2.7 + - - +
265B LYS* 3.8 24.6 + - - +
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Residues in contact with ASN 262 (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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228A ARG* 3.3 58.0 + - - +
229A ASP* 2.9 24.9 + - - +
258B ASN* 3.5 16.3 + - - +
259B TYR* 3.0 12.1 + - + +
261B GLU* 1.3 82.4 - - - +
263B ARG* 1.3 69.4 + - - +
264B PRO* 4.5 1.2 - - - +
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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
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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