Contacts of the strand formed by residues 322 - 330 (chain B) in PDB entry 2G5T
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 TYR 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B SER* 4.3 11.2 - - - -
293B MET* 4.1 8.9 - - + +
316B LEU* 3.5 5.8 - - - +
317B ARG* 3.2 74.6 + - + +
319B ILE 3.7 1.4 + - - -
320B GLN 3.6 0.4 - - - -
321B ASN* 1.3 84.4 - - + +
323B SER* 1.3 63.7 + - - +
324B VAL* 3.6 21.3 - - + +
346B ILE* 3.6 36.4 - - + +
347B GLU 3.7 2.2 - - - -
348B MET* 4.0 28.7 - - + -
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Residues in contact with SER 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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293B MET* 5.3 0.4 - - - -
301B CYS* 5.2 0.4 - - - -
314B GLN* 5.2 2.7 + - - -
315B TRP 3.1 13.2 - - - -
316B LEU* 3.9 7.2 - - - -
322B TYR* 1.3 77.6 - - - +
324B VAL* 1.3 69.5 + - - +
345B HIS 4.7 0.2 - - - -
346B ILE* 3.6 3.1 - - - +
347B GLU* 2.7 56.6 + - - +
354B VAL* 3.7 3.8 - - - +
359B PRO* 3.7 31.0 - - - +
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Residues in contact with VAL 324 (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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290B PRO* 4.0 22.0 - - + -
292B SER* 3.8 13.5 - - - +
293B MET* 3.9 8.9 - - + +
313B LEU 3.6 1.2 - - - +
314B GLN* 3.2 4.6 - - - -
315B TRP* 2.8 40.0 + - + +
322B TYR* 3.6 27.6 - - + +
323B SER* 1.3 79.3 - - - +
325B MET* 1.3 64.5 + - - +
344B GLN* 3.4 38.4 - - + +
345B HIS 3.6 5.4 - - - +
346B ILE* 4.6 7.2 - - + -
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Residues in contact with MET 325 (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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312B SER* 3.6 19.1 - - - +
313B LEU 3.2 9.9 - - - +
314B GLN* 3.8 22.9 - - + +
324B VAL* 1.3 76.0 - - - +
326B ASP* 1.3 64.4 + - - +
327B ILE* 3.3 37.5 - - + -
343B ARG 3.8 0.7 - - - +
344B GLN* 3.1 9.0 - - - +
345B HIS* 2.9 49.4 + - + +
362B PRO* 4.6 9.4 - - + -
364B PHE* 3.7 8.1 - - + -
371B PHE* 3.6 31.6 - - + -
373B LYS* 4.9 6.7 - - - +
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Residues in contact with ASP 326 (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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287B ILE* 5.8 1.6 - - + +
288B THR 4.7 4.9 - - - +
289B ALA* 5.2 1.0 - - - +
290B PRO* 3.1 34.2 - - - +
311B ILE 4.0 0.3 - - - +
312B SER* 3.2 6.6 - - - -
313B LEU* 2.8 38.7 + - + +
315B TRP* 4.6 4.4 + - - +
324B VAL 4.1 1.0 + - - -
325B MET* 1.3 74.9 - - - +
327B ILE* 1.3 62.1 + - - +
328B CYS* 4.0 8.1 - - - -
339B CYS* 3.7 31.8 - - + +
340B LEU 4.9 0.7 - - - +
344B GLN* 3.4 26.7 - - - +
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Residues in contact with ILE 327 (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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306B ALA* 5.7 0.2 - - + -
310B ARG* 3.3 34.1 - - + +
311B ILE 3.7 6.7 - - - +
312B SER* 4.3 2.5 - - - -
325B MET* 3.3 35.4 - - + -
326B ASP* 1.3 73.1 + - - +
328B CYS* 1.3 60.0 + - - +
329B ASP* 4.2 2.6 - - - +
338B ASN 4.0 0.3 - - - +
339B CYS* 3.3 14.8 - - - +
340B LEU 3.8 6.3 + - - -
343B ARG* 3.2 43.5 + - + +
345B HIS* 3.8 8.7 - - + -
364B PHE* 4.5 8.1 - - + -
371B PHE* 3.9 0.9 - - + -
389B ILE* 3.8 28.9 - - + -
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Residues in contact with CYS 328 (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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287B ILE* 3.9 29.2 - - + -
309B GLU 3.7 0.5 - - - +
310B ARG* 3.3 3.3 - - - +
311B ILE* 2.9 40.6 + - + +
313B LEU* 5.0 3.8 - - - -
326B ASP* 4.0 11.2 - - - -
327B ILE* 1.3 74.9 - - - +
329B ASP* 1.3 67.2 + - - +
337B TRP* 3.7 7.8 - - + -
338B ASN 3.1 7.9 - - - +
339B CYS* 2.0 45.5 - - - -
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Residues in contact with ASP 329 (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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309B GLU* 3.3 4.5 - - + +
310B ARG* 2.7 52.0 + - - +
327B ILE 4.2 1.7 - - - +
328B CYS* 1.3 77.0 - - - +
330B TYR* 1.3 69.0 - - - +
331B ASP* 3.6 0.7 + - - +
337B TRP* 3.5 6.2 - - - -
338B ASN* 2.8 33.7 + - + +
343B ARG* 3.0 24.2 + - - +
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Residues in contact with TYR 330 (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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222B PHE* 3.9 26.7 - + + -
272B ASN* 4.8 6.6 + - + -
309B GLU* 3.0 43.7 + - + +
329B ASP* 1.3 76.2 - - - +
331B ASP* 1.3 64.3 + - - +
332B GLU* 3.2 46.7 + - - -
335B GLY* 3.4 33.1 - - - -
336B ARG 3.9 4.5 - - - -
337B TRP* 3.5 37.6 - + + -
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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