Contacts of the strand formed by residues 312 - 319 (chain A) in PDB entry 3H8E
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 ASN 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A TYR 3.4 2.5 - - - -
253A GLN* 3.4 35.8 + - - +
254A GLY 3.3 7.9 - - - +
255A GLY* 2.8 30.0 + - - +
256A LYS 2.9 21.8 - - - +
257A LYS 4.4 1.7 - - - +
259A ASP* 3.0 19.9 - - + +
260A LYS 4.7 1.7 + - - +
261A PRO* 3.2 19.3 - - + +
262A PHE* 2.9 32.7 + - - -
311A VAL* 1.3 71.9 - - - +
313A LEU* 1.3 59.7 + - - +
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A LEU 3.6 2.9 - - - +
251A ASN 3.7 0.2 - - - -
252A TYR* 2.8 52.6 + - + +
262A PHE* 3.3 22.0 - - + +
264A LEU* 3.9 29.6 - - + -
301A LEU* 4.0 27.6 - - + +
304A VAL* 4.1 15.7 - - + -
311A VAL* 3.7 7.1 + - + -
312A ASN* 1.3 72.8 - - - +
314A VAL* 1.4 60.5 + - - +
315A CYS* 3.9 14.3 - - - -
491A LEU* 4.0 26.9 - - + -
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A VAL* 4.3 8.3 - - + -
250A LEU 3.5 3.4 - - - +
251A ASN* 3.8 30.1 - - - +
253A GLN* 4.9 2.0 - - - +
261A PRO* 4.1 18.8 - - + -
262A PHE 2.9 6.7 + - - +
263A VAL* 3.1 16.8 - - + +
264A LEU 2.9 24.9 + - - -
313A LEU* 1.4 71.9 - - - +
315A CYS* 1.3 63.1 + - - +
316A LEU* 4.0 13.9 - - + -
366A PHE* 3.8 46.2 - - + -
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Residues in contact with CYS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ILE 3.4 0.7 - - - +
249A VAL* 3.3 6.4 - - - +
250A LEU* 2.8 56.1 + - + +
264A LEU* 3.4 5.8 - - - -
297A VAL* 3.5 29.2 - - + -
301A LEU* 4.1 25.6 - - + -
313A LEU* 3.9 24.7 - - - -
314A VAL* 1.3 75.2 - - - +
316A LEU* 1.4 64.6 + - - +
317A LEU* 4.1 0.7 - - + -
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LEU* 4.4 3.6 - - + -
248A ILE 3.3 2.7 - - - -
249A VAL* 3.9 31.6 - - + -
263A VAL* 3.8 17.5 - - + -
264A LEU 2.8 12.3 + - - +
265A VAL* 3.3 5.9 - - + +
266A GLY 2.9 25.1 + - - -
314A VAL* 4.0 8.5 - - + -
315A CYS* 1.4 82.0 - - - +
317A LEU* 1.3 64.1 + - - +
318A ALA 3.9 0.9 + - - -
359A THR* 3.6 27.8 - - + +
362A TYR* 4.1 9.2 - - + -
363A ALA* 3.7 36.8 - - + +
366A PHE* 4.0 8.7 - - + -
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ARG 3.5 1.0 - - - +
247A LEU* 3.5 5.2 - - - +
248A ILE* 2.8 44.6 + - + +
250A LEU* 3.9 22.4 - - + -
266A GLY 3.7 3.6 - - - +
294A ALA* 3.9 17.9 - - + +
297A VAL* 3.6 37.9 - - + -
298A PHE* 3.2 44.2 - - + +
316A LEU* 1.3 77.7 - - - +
318A ALA* 1.3 60.2 + - - +
319A CYS* 3.4 19.8 + - - -
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Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A PHE* 3.9 13.9 - - + -
246A ARG 4.2 0.2 - - - -
247A LEU* 4.3 3.8 - - - -
266A GLY 3.0 15.7 + - - +
268A GLY* 2.9 21.0 + - - -
316A LEU 3.9 1.4 + - - -
317A LEU* 1.3 68.3 - - - +
319A CYS* 1.3 61.8 + - - +
355A VAL* 3.7 29.5 - - + +
356A LEU* 4.7 5.4 - - + -
359A THR* 3.4 28.3 - - + +
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Residues in contact with CYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PRO* 3.7 22.2 - - + -
202A LEU* 3.8 1.6 - - + -
234A PHE* 3.7 3.1 - - - -
245A PRO* 3.2 7.1 - - - +
246A ARG* 2.9 42.8 + - + +
248A ILE* 3.9 13.5 - - - -
268A GLY* 3.0 12.3 - - - +
291A MET* 3.6 27.8 - - - -
317A LEU* 3.8 24.5 - - - -
318A ALA* 1.3 75.2 - - - +
320A ALA* 1.3 63.1 - - - +
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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