Contacts of the strand formed by residues 246 - 253 (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 ARG 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A PRO* 3.7 33.6 - - + +
200A SER* 3.6 23.8 + - - +
203A ALA* 4.2 4.7 - - + +
220A VAL* 3.7 22.1 - - + +
221A LEU 3.4 8.3 - - - +
222A ASP* 3.6 24.6 - - - +
223A GLU* 3.9 2.4 - - - +
226A ILE* 4.2 0.2 - - - -
234A PHE* 3.6 4.6 - - - -
244A PRO* 3.5 26.5 - - - +
245A PRO* 1.3 99.1 + - - +
247A LEU* 1.3 59.7 + - - +
248A ILE* 4.0 15.0 + - + -
317A LEU 3.5 1.4 - - - +
319A CYS* 2.9 35.3 + - + +
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Residues in contact with LEU 247 (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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220A VAL* 3.6 0.9 - - - -
221A LEU* 2.8 69.1 + - + +
226A ILE* 3.8 5.0 - - + +
231A MET* 3.6 35.2 - - + -
234A PHE* 4.1 11.4 - - + -
246A ARG* 1.3 71.7 - - - +
248A ILE* 1.3 62.5 + - - +
249A VAL* 4.8 4.5 - - + -
316A LEU* 4.4 5.4 - - + -
317A LEU 3.5 20.4 - - - +
318A ALA* 4.3 1.3 - - - -
359A THR* 3.8 31.2 - - + +
362A TYR* 4.1 14.4 - - + -
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Residues in contact with ILE 248 (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 4.5 2.0 - - - +
202A LEU* 3.6 19.5 - - + +
203A ALA* 3.5 40.4 - - + +
206A ALA* 3.4 26.9 - - + -
218A VAL* 4.5 3.8 - - + -
219A GLU 3.7 7.2 - - - +
220A VAL* 4.5 4.9 - - + +
246A ARG* 4.2 7.6 - - + -
247A LEU* 1.3 78.0 - - - +
249A VAL* 1.3 63.0 + - - +
250A LEU* 3.8 13.9 - - + -
315A CYS 3.4 1.2 - - - +
316A LEU* 3.3 5.2 - - - -
317A LEU* 2.8 48.9 + - + +
319A CYS* 3.9 16.2 - - - -
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Residues in contact with VAL 249 (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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217A LYS 3.8 0.9 - - - +
218A VAL* 3.2 7.1 - - - +
219A GLU* 2.8 47.1 + - + +
221A LEU* 3.8 24.9 - - + -
247A LEU* 4.6 4.0 - - + +
248A ILE* 1.3 76.6 - - - +
250A LEU* 1.3 65.7 + - - +
251A ASN* 4.8 7.0 - - + +
314A VAL* 4.3 6.3 - - + -
315A CYS 3.3 3.8 - - - +
316A LEU* 3.9 24.0 - - + -
362A TYR* 4.0 16.6 - - + +
366A PHE* 4.2 16.8 - - + -
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Residues in contact with LEU 250 (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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206A ALA* 3.8 25.1 - - + +
209A LEU* 4.2 7.2 - - + -
216A LEU* 4.1 6.6 - - + +
217A LYS 3.6 3.8 - - - -
218A VAL* 3.9 14.4 - - + -
248A ILE* 3.8 21.5 - - + -
249A VAL* 1.3 77.0 - - - +
251A ASN* 1.4 59.8 + - - +
252A TYR* 3.9 0.8 + - - +
298A PHE* 4.1 10.1 - - + -
301A LEU* 3.8 29.6 - - + -
313A LEU 3.6 2.9 - - - +
314A VAL* 3.5 2.0 - - - -
315A CYS* 2.8 56.3 + - + +
317A LEU* 3.9 22.2 - - + -
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Residues in contact with ASN 251 (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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215A ALA 3.5 2.3 - - - +
216A LEU* 3.5 4.9 - - - +
217A LYS* 2.8 50.8 + - + +
249A VAL* 4.1 9.1 - - + +
250A LEU* 1.4 72.4 - - - +
252A TYR* 1.3 61.3 + - - +
253A GLN* 2.9 37.2 + - - +
313A LEU 3.7 2.5 - - - -
314A VAL* 3.8 23.0 - - + +
366A PHE* 4.2 15.0 - - - -
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Residues in contact with TYR 252 (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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215A ALA* 3.4 31.4 - - + -
216A LEU* 3.8 12.9 - - + +
250A LEU 3.9 0.2 + - - -
251A ASN* 1.3 74.1 - - - +
253A GLN* 1.4 61.4 + - - +
254A GLY* 3.7 10.5 - - - -
301A LEU* 4.1 11.4 - - + -
304A VAL* 3.6 26.7 - - + -
305A LEU* 3.6 30.1 - - + -
308A GLN* 3.4 21.9 + - + +
309A LEU 2.6 29.8 + - - -
311A VAL* 3.2 16.4 - - + -
312A ASN* 3.4 2.6 - - - -
313A LEU* 2.8 49.0 + - + +
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Residues in contact with GLN 253 (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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215A ALA* 3.0 25.8 + - - +
251A ASN* 2.9 36.0 + - - +
252A TYR* 1.4 69.4 + - - +
254A GLY* 1.3 60.7 + - - +
255A GLY 3.5 4.8 - - - +
257A LYS* 4.9 20.4 + - - +
261A PRO* 5.3 2.0 - - - +
312A ASN* 3.4 34.2 + - - +
314A VAL* 4.9 4.6 - - - +
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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