Contacts of the strand formed by residues 278 - 283 (chain B) in PDB entry 1GQF
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 LYS 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230B PHE* 3.7 10.3 - - + -
265B PHE* 3.4 34.8 - - + +
267B GLY* 5.0 5.4 - - - +
270B CYS 5.2 0.9 - - - -
273B LEU* 3.0 41.4 + - + -
274B LEU* 4.8 1.9 - - - +
275B GLU 4.6 1.6 - - - +
276B LYS 2.6 28.0 + - - +
277B PRO* 1.3 75.5 - - - +
279B LEU* 1.3 62.0 + - - +
280B PHE* 3.4 24.2 - - + -
324B GLU* 5.4 0.7 - - - -
325B ALA 4.1 4.2 + - - -
326B ASP* 2.8 28.5 + - - +
327B PHE* 3.5 23.6 - - + -
328B LEU 3.2 19.8 + - - -
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Residues in contact with LEU 279 (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 PHE* 4.7 2.5 - - + -
229B CYS* 4.9 3.1 - - - -
230B PHE* 2.8 17.1 + - - +
231B ALA* 3.3 8.6 - - + -
232B CYS* 2.9 25.3 + - - +
277B PRO* 4.1 12.1 - - + -
278B LYS* 1.3 74.5 - - - +
280B PHE* 1.3 65.4 + - - +
281B PHE* 3.5 28.3 - - + -
328B LEU* 3.7 29.4 - - + +
366B ILE* 5.0 2.2 - - + -
394B LEU* 4.9 2.2 - - + -
398B LEU* 3.7 33.7 - - + -
400B PHE* 3.7 24.7 - - + -
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Residues in contact with PHE 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 5.3 2.9 - - + -
230B PHE* 4.3 9.4 - + - -
232B CYS* 3.3 35.2 - - + +
234B LEU* 5.7 5.4 - - + -
261B LEU 5.0 1.1 - - - -
262B THR* 3.6 32.1 - - + -
265B PHE* 3.9 28.9 - + - -
278B LYS* 3.4 22.9 - - + -
279B LEU* 1.3 74.0 - - - +
281B PHE* 1.3 64.2 + - - +
282B ILE* 3.8 8.8 + - + +
327B PHE* 3.5 25.4 - + - -
328B LEU* 2.9 13.6 + - - +
329B PHE* 3.4 28.4 - + + +
330B ALA 3.1 23.0 + - - -
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Residues in contact with PHE 281 (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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193B PHE* 3.9 25.8 - + - -
231B ALA* 4.6 2.9 - - + -
232B CYS 2.8 13.2 + - - +
233B ILE* 3.1 29.4 - - + +
234B LEU 3.0 23.4 + - - -
279B LEU* 3.5 38.6 - - + -
280B PHE* 1.3 73.5 - - - +
282B ILE* 1.3 60.8 + - - +
328B LEU* 4.9 3.8 - - + -
330B ALA* 3.8 20.4 - - + +
349B PHE* 5.0 4.7 - + + -
353B LEU* 3.9 31.9 - - + -
357B LEU* 6.0 0.2 - - + -
366B ILE* 4.4 12.1 - - + -
370B LEU* 4.0 25.4 - - + -
400B PHE* 5.3 2.0 - + - -
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Residues in contact with ILE 282 (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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234B LEU* 3.7 33.0 - - + +
243B ILE* 4.7 4.5 - - + -
258B ILE* 4.7 10.8 - - + -
262B THR* 5.6 2.5 - - + -
280B PHE* 4.3 12.3 - - + +
281B PHE* 1.3 80.1 - - - +
283B GLN* 1.3 62.8 + - - +
284B ALA* 3.9 23.1 - - + +
329B PHE* 4.6 7.2 - - + -
330B ALA 2.9 17.0 + - - +
331B TYR* 3.4 49.4 - - + +
332B SER* 2.9 30.2 + - - +
349B PHE* 3.7 4.5 - - - -
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Residues in contact with GLN 283 (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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185B ASP* 5.1 2.9 - - - +
234B LEU 2.9 8.9 + - - +
235B LEU* 3.8 23.7 - - + +
236B SER 3.1 24.8 + - - +
282B ILE* 1.3 71.8 - - - +
284B ALA* 1.3 59.4 + - - +
285B ALA* 4.2 5.4 + - - +
332B SER* 2.9 37.1 + - - +
334B VAL* 2.9 24.8 + - - +
335B PRO 4.4 0.7 - - - +
347B SER* 3.8 24.5 + - - +
349B PHE* 3.5 17.7 - - + +
350B VAL* 4.3 8.7 - - + -
1403B SO4 4.4 8.6 + - - +
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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