Contacts of the strand formed by residues 263 - 269 (chain B) in PDB entry 2GTP
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 SER 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B THR* 3.1 16.6 + - - +
220B ALA* 4.4 4.3 - - - -
221B ILE 2.9 26.9 + - - -
261B ASP 4.1 1.0 + - - -
262B THR* 1.3 69.7 - - - +
264B ILE* 1.3 59.5 + - - +
265B ILE* 3.3 20.4 - - - +
320B TYR* 4.4 7.9 - - - -
342B VAL* 4.4 4.6 + - - +
343B ILE* 4.7 7.4 - - - +
346B ASN* 2.9 36.9 + - - +
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Residues in contact with ILE 264 (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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221B ILE* 3.7 34.8 - - + +
223B PHE* 5.3 2.7 - - + -
250B PHE* 3.7 29.8 - - + -
253B ILE* 4.5 3.1 - - + +
254B CYS* 4.4 18.2 - - - +
259B PHE* 4.2 15.5 - - + -
262B THR* 3.3 2.8 + - + +
263B SER* 1.3 70.6 - - - +
265B ILE* 1.3 66.4 + - - +
317B LYS* 3.5 27.5 - - + +
318B GLU 4.7 3.5 + - - +
319B ILE* 3.6 19.1 - - + +
320B TYR* 3.0 29.7 + - - -
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Residues in contact with ILE 265 (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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220B ALA* 4.5 9.6 - - + -
221B ILE 2.8 15.5 + - - +
222B ILE* 3.4 7.1 - - + -
223B PHE* 2.7 34.8 + - - +
263B SER* 3.3 33.2 - - - +
264B ILE* 1.3 77.5 - - - +
266B LEU* 1.3 59.1 + - - +
267B PHE* 3.4 32.1 - - + -
320B TYR* 3.3 27.4 - - + +
322B HIS* 4.1 4.0 - - + -
339B VAL* 3.8 30.7 - - + -
342B VAL* 5.0 5.2 - - + -
343B ILE* 5.2 1.6 - - + -
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Residues in contact with LEU 266 (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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223B PHE* 3.4 25.4 - - + +
225B VAL* 3.7 26.0 - - + -
250B PHE* 4.5 11.4 - - + -
264B ILE 4.2 0.2 - - - -
265B ILE* 1.3 73.4 - - - +
267B PHE* 1.3 62.7 + - - +
268B LEU* 3.9 18.4 - - + -
304B GLN 5.3 0.2 - - - +
307B PHE* 3.7 32.5 - - + -
308B GLU* 5.1 4.0 - - + -
319B ILE* 3.8 21.5 - - + -
320B TYR 2.9 9.4 + - - +
321B THR* 3.3 19.1 - - + +
322B HIS 2.9 26.7 + - - +
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Residues in contact with PHE 267 (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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49B ILE* 3.9 33.4 - - + -
53B MET* 6.0 0.2 - - + -
222B ILE* 3.6 34.8 - - + -
223B PHE 2.9 12.8 + - - +
224B CYS* 4.3 9.2 - - - -
225B VAL* 3.0 27.0 + - - +
265B ILE* 3.4 26.0 - - + -
266B LEU* 1.3 75.7 - - - +
268B LEU* 1.3 62.1 + - - +
269B ASN* 3.3 5.0 + - + +
322B HIS* 3.4 7.2 - + + -
324B THR* 3.7 25.4 - - + +
332B VAL* 5.5 3.8 - - + -
335B VAL* 3.3 33.0 - - + -
336B PHE* 5.1 5.2 - + + -
339B VAL* 3.8 11.0 - - + -
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Residues in contact with LEU 268 (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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225B VAL* 3.8 27.1 - - + -
227B LEU* 3.5 22.7 - - + +
266B LEU* 3.9 23.3 - - + -
267B PHE* 1.3 68.9 - - - +
269B ASN* 1.3 63.1 + - - +
303B ILE* 5.0 0.4 - - + -
304B GLN* 3.9 22.7 - - + +
307B PHE* 4.5 9.9 - - + -
321B THR* 3.8 22.4 - - + -
322B HIS 2.9 9.5 + - - +
323B PHE* 3.4 42.4 - - + +
324B THR* 3.0 20.1 + - - +
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Residues in contact with ASN 269 (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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44B SER 3.1 23.7 + - - +
45B GLY* 3.9 3.4 - - - -
49B ILE* 5.9 1.8 - - - -
224B CYS* 5.1 3.8 - - + +
225B VAL 2.7 17.5 + - - +
227B LEU* 2.9 27.4 + - - +
267B PHE* 4.1 8.7 - - + +
268B LEU* 1.3 71.1 - - - +
270B LYS* 1.3 75.4 + - + +
271B LYS 3.2 2.7 - - - -
324B THR* 2.9 20.1 + - - +
326B ALA* 2.9 34.8 + - - +
403B GDP 3.2 26.0 + - - -
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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