Contacts of the strand formed by residues 251 - 256 (chain D) in PDB entry 4GID
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 ILE 251 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D VAL* 4.9 0.2 - - + -
250D ILE* 1.3 73.0 - - - +
252D VAL* 1.3 63.4 + - - +
253D ARG 3.7 17.5 - - - +
254D VAL* 4.0 11.4 - - + -
265D CYS 3.8 5.5 - - - +
268D TYR* 3.9 18.3 - - + +
269D ASN* 2.7 38.6 + - - +
273D SER* 3.8 13.2 - - - +
284D LEU* 5.9 1.3 - - + -
333D LEU* 4.2 22.9 - - + -
334D TYR 3.3 13.5 - - - +
335D LEU* 3.8 17.7 - - + -
379D THR* 3.7 32.1 - - + +
381D MET* 4.6 6.1 - - - -
430D CYS* 4.2 0.9 - - - +
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Residues in contact with VAL 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D ILE* 4.2 12.3 - - + -
251D ILE* 1.3 77.1 - - - +
253D ARG* 1.3 60.4 + - + +
265D CYS* 3.6 17.8 - - - +
268D TYR* 4.2 1.8 - - - -
334D TYR* 2.7 38.1 + - + +
335D LEU 4.2 0.4 - - - +
336D MET* 4.2 16.2 - - + +
343D SER* 4.1 18.2 - - - +
425D LEU* 5.3 4.3 - - + -
427D MET* 3.8 33.5 + - + -
430D CYS* 4.1 16.3 - - - -
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Residues in contact with ARG 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ASN* 4.6 12.1 - - - +
413B PHE* 3.8 38.1 - - - -
251D ILE* 3.7 3.9 - - - +
252D VAL* 1.3 83.3 - - + +
254D VAL* 1.3 73.1 + - - +
255D GLU* 2.7 30.3 + - - +
258D GLY 4.7 0.2 + - - -
260D ASP* 3.0 46.1 + - - +
268D TYR* 3.7 9.1 - - - -
333D LEU* 3.7 0.2 - - - -
334D TYR* 2.8 57.5 + - + -
425D LEU* 6.6 0.4 - - - -
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Residues in contact with VAL 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ILE* 4.0 5.6 - - + -
253D ARG* 1.3 80.9 - - - +
255D GLU* 1.3 71.8 + - - +
256D ILE* 4.5 8.3 - - + -
260D ASP* 3.6 4.9 - - - +
261D LEU* 2.9 45.3 + - + +
268D TYR* 3.5 41.8 + - + -
284D LEU* 6.2 4.0 - - + -
288D VAL* 5.1 5.2 - - + -
292D ALA* 5.9 1.6 - - + -
331D ILE* 4.7 3.1 - - + -
332D SER 3.4 10.5 - - - +
333D LEU* 3.9 22.0 - - + -
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Residues in contact with GLU 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B PHE* 3.9 6.5 - - - +
253D ARG* 2.7 39.8 + - - +
254D VAL* 1.3 77.9 - - - +
256D ILE* 1.3 72.2 + - - +
257D ASN 4.0 0.4 - - - -
258D GLY* 3.3 33.3 + - - +
259D GLN 3.3 9.9 - - - +
260D ASP* 4.2 1.6 - - - -
261D LEU 4.5 0.2 - - - +
331D ILE* 3.6 2.4 - - - +
332D SER* 3.1 41.4 + - - +
334D TYR* 2.6 35.1 + - + -
345D ARG* 4.4 6.1 + - - -
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Residues in contact with ILE 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D VAL* 4.5 8.3 - - + -
255D GLU* 1.3 82.8 - - - +
257D ASN* 1.3 72.4 + - + +
259D GLN* 3.0 23.1 + - - +
261D LEU* 4.2 14.1 - - + -
292D ALA* 4.5 12.3 - - + +
295D SER* 3.4 33.7 + - - +
296D ILE* 3.9 21.3 - - + +
299D ALA* 5.1 1.8 - - + -
329D PRO* 3.4 32.1 - - + -
330D VAL 3.7 2.9 - - - +
331D ILE* 4.1 22.7 - - + -
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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