Contacts of the strand formed by residues 296 - 305 (chain B) in PDB entry 2G4C
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 GLY 296 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292B ASN* 4.0 6.6 + - - -
293B PHE* 2.5 30.4 + - - +
294B PRO 3.7 0.6 - - - -
295B TRP* 1.3 80.1 - - - +
297B LYS* 1.3 70.5 + - - +
298B GLU* 3.5 9.4 + - - +
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Residues in contact with LYS 297 (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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274B SER* 4.1 22.4 + - - +
290B TYR* 4.2 25.9 - - + -
291B TYR 3.6 8.3 - - - -
292B ASN* 3.8 31.2 + - + +
296B GLY* 1.3 76.3 - - - +
298B GLU* 1.3 66.1 + - - +
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Residues in contact with GLU 298 (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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92B LEU* 3.6 30.8 - - + +
290B TYR* 3.5 5.5 - - - -
291B TYR* 2.9 27.8 + - - +
293B PHE* 3.3 27.6 - - + -
295B TRP* 3.5 21.3 + - - -
296B GLY 3.7 0.7 - - - +
297B LYS* 1.3 82.1 - - - +
299B LEU* 1.3 66.8 + - - +
300B ILE* 4.0 2.8 - - - +
344B ARG* 3.9 16.7 + - - +
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Residues in contact with LEU 299 (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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288B LYS* 3.9 26.5 - - + -
289B LEU 3.0 22.4 - - - +
290B TYR* 3.8 22.0 - - + +
298B GLU* 1.3 75.4 - - - +
300B ILE* 1.3 64.6 + - - +
301B GLU 3.5 18.2 - - - +
302B THR* 3.4 22.9 - - + -
341B ASP* 5.2 0.7 - - - +
344B ARG* 3.0 36.6 + - - +
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Residues in contact with ILE 300 (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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263B TRP* 3.6 33.0 - - + +
273B PHE* 3.4 38.8 - - + -
289B LEU* 3.0 23.9 + - + +
290B TYR 4.4 2.9 - - - +
291B TYR* 4.2 13.9 - - + -
293B PHE* 5.2 1.1 - - + -
298B GLU 4.0 7.9 - - - +
299B LEU* 1.3 81.7 - - - +
301B GLU* 1.3 62.8 + - - +
302B THR* 5.5 0.2 - - - -
339B ASN 4.1 0.2 - - - +
340B GLY* 3.3 1.2 - - - -
341B ASP* 2.6 41.8 + - - +
344B ARG* 4.0 27.8 - - + +
345B GLY* 4.7 1.8 - - - +
348B ALA* 4.9 0.9 - - + -
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Residues in contact with GLU 301 (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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114B TRP* 4.2 4.7 + - - -
237B ALA 5.0 0.2 - - - +
259B ARG* 2.6 51.8 + - - +
263B TRP* 2.7 28.6 + - + +
288B LYS* 3.5 1.2 - - - -
289B LEU* 2.6 50.5 + - + +
299B LEU* 3.5 2.7 - - - +
300B ILE* 1.3 85.0 - - - +
302B THR* 1.3 67.9 + - - +
303B LEU* 4.7 0.9 - - + -
338B VAL* 3.4 13.8 - - + +
339B ASN 3.1 18.2 - - - +
340B GLY* 3.7 14.0 + - - -
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Residues in contact with THR 302 (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 ASN 3.7 7.6 - - - -
288B LYS* 4.4 9.2 - - + -
299B LEU* 3.4 32.1 - - + -
300B ILE 5.5 0.2 - - - -
301B GLU* 1.3 80.2 - - - +
303B LEU* 1.3 65.6 + - - +
304B TRP* 4.4 18.7 - - - -
337B SER 3.7 2.3 + - - +
339B ASN* 2.8 47.0 + - - +
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Residues in contact with LEU 303 (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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252B LEU* 4.0 17.5 - - + -
255B TRP* 3.8 17.9 - - + +
256B LEU* 3.6 41.3 - - + +
259B ARG* 4.3 4.3 - - + -
286B GLY* 4.2 0.4 - - - -
287B ASN* 3.0 34.2 + - - +
289B LEU* 3.2 35.2 - - + -
301B GLU* 4.6 3.8 - - + +
302B THR* 1.3 78.7 - - - +
304B TRP* 1.3 78.3 + - - +
337B SER 3.4 6.1 - - - +
338B VAL* 4.0 16.8 - - + -
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Residues in contact with TRP 304 (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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252B LEU* 4.3 7.2 - - - +
278B CYS* 3.7 17.5 - - + -
279B GLN* 3.7 22.0 - - - -
280B ASP 4.0 5.8 - - - -
281B GLU* 3.6 54.8 + - + -
282B GLU 6.3 0.2 - - - -
283B GLY 4.8 5.2 - - - -
284B ARG 5.3 0.2 - - - -
285B LYS 3.4 22.9 - - - -
286B GLY* 3.5 18.2 - - - -
287B ASN 5.4 0.4 - - - -
288B LYS* 3.8 23.0 - - - +
302B THR* 4.4 19.7 + - - -
303B LEU* 1.3 88.2 + - - +
305B ASN* 1.3 60.9 + - - +
306B LEU* 3.7 18.6 + - + -
336B LEU* 3.3 4.9 - - - +
337B SER* 2.7 44.0 + - - +
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Residues in contact with ASN 305 (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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248B SER* 2.5 45.9 + - - -
249B ASN* 3.6 10.7 - - - +
252B LEU* 4.6 12.2 - - + +
283B GLY* 4.2 1.0 - - - -
284B ARG 3.8 26.8 + - - +
285B LYS* 3.1 21.5 + - + +
304B TRP* 1.3 72.2 - - - +
306B LEU* 1.3 61.6 + - - +
307B GLY* 3.3 17.3 + - - -
334B CYS* 4.1 4.1 - - - +
335B VAL 4.1 2.9 - - - +
336B LEU* 4.3 9.9 - - + +
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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