Contacts of the strand formed by residues 254 - 259 (chain G) in PDB entry 2I3T
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 VAL 254 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197G ARG* 3.3 12.9 - - - +
212G SER* 2.8 44.2 + - - -
213G SER 3.0 9.8 + - - +
216G GLY* 3.7 27.6 - - - -
217G ARG 3.8 11.2 - - - +
218G VAL* 4.3 3.8 - - + -
240G CYS* 4.1 4.9 - - - -
241G HIS* 3.7 29.2 - - + -
252G TYR 4.0 0.7 - - - +
253G PRO* 1.3 69.2 - - - +
255G ASN* 1.3 58.1 + - - +
257G ILE* 4.0 6.1 - - + -
268G THR* 3.9 17.3 - - - -
269G ALA 3.6 9.2 - - - +
270G GLY* 4.2 0.9 - - - -
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Residues in contact with ASN 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G TYR* 5.8 0.4 - - - -
106G ARG* 5.3 0.7 + - - -
197G ARG* 2.7 50.3 + - - +
198G ASP* 3.7 16.3 - - - +
253G PRO* 3.5 10.4 - - - +
254G VAL* 1.3 71.9 - - - +
256G SER* 1.3 58.9 + - - +
269G ALA 2.9 6.3 + - - -
270G GLY 3.6 0.6 - - - -
271G SER* 3.1 32.3 + - - +
296G SER* 4.4 0.6 - - - -
297G VAL 3.1 23.6 + - - +
298G VAL* 3.8 23.1 - - + +
299G LYS* 5.2 2.6 + - - -
314G ASP* 4.1 7.8 + - - +
381H LEU* 4.7 1.4 - - - +
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Residues in contact with SER 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198G ASP* 3.4 9.5 + - - -
254G VAL 3.6 1.0 - - - -
255G ASN* 1.3 81.5 - - - +
257G ILE* 1.3 65.2 + - - +
258G GLU* 5.5 0.2 + - - -
268G THR* 3.5 0.9 - - - -
269G ALA* 2.8 37.8 + - - +
298G VAL 3.8 15.5 - - - -
299G LYS* 3.7 14.4 + - - +
300G ILE* 3.3 39.1 + - - +
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Residues in contact with ILE 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198G ASP* 3.0 27.7 + - + +
199G VAL 5.1 0.2 - - - +
200G ALA* 4.0 22.5 - - + +
210G ALA* 3.6 39.3 - - + +
211G CYS* 3.9 13.0 - - - +
212G SER* 3.6 23.8 - - - +
218G VAL* 4.7 2.2 - - + -
254G VAL* 4.0 3.4 - - + -
256G SER* 1.3 81.2 + - - +
258G GLU* 1.3 68.1 + - - +
266G LEU* 4.2 10.8 - - + -
267G TYR 3.2 7.2 - - - +
268G THR* 3.6 21.8 - - + -
300G ILE* 4.5 0.7 - - - -
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Residues in contact with GLU 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200G ALA* 4.8 5.2 - - - -
256G SER* 5.5 0.2 + - - -
257G ILE* 1.3 79.3 - - - +
259G PHE* 1.3 73.0 + - - +
266G LEU* 3.6 5.0 - - - +
267G TYR* 2.7 41.2 + - - +
300G ILE* 3.4 23.2 - - + +
301G ALA* 3.5 6.6 - - - +
302G CYS* 2.7 48.5 + - + +
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Residues in contact with PHE 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200G ALA* 4.0 19.9 - - + +
201G LEU 3.5 26.2 - - - -
202G LEU* 3.7 17.9 - - + -
203G PRO* 3.7 32.1 - - + -
206G GLN* 6.0 0.2 - - - -
210G ALA* 4.2 3.4 - - + -
258G GLU* 1.3 86.6 - - - +
260G SER* 1.3 65.6 + - - +
261G PRO* 3.8 3.8 - - - +
264G LYS* 3.8 7.0 - - - +
265G PHE 3.1 19.1 - - - -
266G LEU* 3.5 26.7 - - + -
280G LEU* 3.5 33.2 - - + -
281G GLN* 5.6 2.0 - - - -
302G CYS* 4.0 4.6 - - - +
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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