Contacts of the strand formed by residues 318 - 323 (chain B) in PDB entry 2G1Y
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 PHE 318 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B LYS* 4.1 12.6 - - - -
272B TYR* 3.5 44.9 - + + -
273B THR 3.8 15.0 - - - -
274B LEU* 3.8 12.6 - - + -
314B PHE* 3.0 29.7 + + + +
315B ILE* 2.9 19.6 - - - +
317B LYS* 1.3 103.6 - - + +
319B TYR* 1.3 65.3 + - - +
320B THR* 3.2 11.3 + - - -
331B PHE* 4.1 18.4 - - + -
332B ALA* 3.2 20.2 - - - +
333B LEU* 4.2 17.5 - - + -
334B ALA* 4.1 0.2 - - - -
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Residues in contact with TYR 319 (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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154B SER* 3.3 30.0 - - - -
155B PHE 3.8 11.9 - - - -
156B TYR* 3.9 18.7 - + + +
170B GLN* 4.7 1.9 + - - -
172B VAL* 4.2 5.5 - - - +
176B SER* 3.0 21.1 + - - -
177B ASP* 2.7 41.5 + - + +
180B HIS* 3.3 35.7 - - + +
181B TYR* 3.5 21.8 - + + -
185B PHE* 3.6 17.0 - + - -
315B ILE 4.5 1.8 - - - -
318B PHE* 1.3 72.3 - - - +
320B THR* 1.3 61.0 + - - +
330B GLY 3.8 0.2 - - - +
331B PHE* 3.5 6.2 - - - -
332B ALA* 2.7 27.7 + - + +
334B ALA* 3.5 9.2 - - + +
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Residues in contact with THR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PHE 4.1 0.2 - - - +
154B SER* 3.2 5.9 - - - -
155B PHE* 2.8 44.1 + - - -
220B VAL* 4.3 2.0 - - + -
315B ILE* 3.9 14.1 - - - +
318B PHE 3.2 10.6 + - - -
319B TYR* 1.3 77.4 - - - +
321B GLU* 1.3 62.7 + - - +
322B PHE* 3.4 31.9 + - + -
329B ILE* 3.7 18.8 - - + -
330B GLY 3.4 9.2 - - - +
331B PHE* 3.1 20.7 - - + -
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Residues in contact with GLU 321 (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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150B GLU* 5.4 3.8 - - - +
152B VAL* 4.2 31.7 - - + +
154B SER* 3.5 14.1 - - - +
176B SER* 3.5 22.5 + - - -
185B PHE* 3.8 24.3 - - + -
187B TYR* 2.9 35.9 + - + -
320B THR* 1.3 74.8 - - - +
322B PHE* 1.3 63.9 + - - +
323B ASP* 3.8 3.2 + - - +
329B ILE* 3.4 7.3 - - - +
330B GLY* 2.8 37.0 + - - +
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Residues in contact with PHE 322 (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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34B THR* 3.6 24.9 - - + -
152B VAL* 3.0 7.8 - - - -
153B PHE* 2.7 72.0 + + + -
155B PHE* 4.0 8.5 - + - -
196B TRP* 3.4 38.1 - + + -
220B VAL* 3.6 38.6 - - + -
222B THR* 3.7 19.1 - - + -
320B THR* 3.4 18.6 - - + -
321B GLU* 1.3 73.0 - - - +
323B ASP* 1.3 59.4 + - - +
324B ARG 3.6 2.5 + - - -
328B ARG 4.2 1.8 - - - -
329B ILE* 4.0 9.6 - - + -
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Residues in contact with ASP 323 (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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152B VAL* 3.4 20.8 - - + +
187B TYR* 4.3 9.5 - - + -
196B TRP* 3.9 3.6 - - - -
321B GLU* 3.8 3.4 + - - +
322B PHE* 1.3 68.4 - - - +
324B ARG* 1.3 58.3 + - - +
325B ARG* 3.2 13.9 + - - +
326B ASN* 3.0 26.4 + - - +
327B ASN* 2.9 23.6 + - - -
328B ARG* 2.9 60.1 + - + +
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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