Contacts of the strand formed by residues 257 - 263 (chain A) in PDB entry 2HRC
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 VAL 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A GLU 3.9 2.5 - - - +
256A VAL* 1.3 73.4 - - - +
258A ILE* 1.3 72.4 + - - +
259A LEU* 4.6 3.8 - - + -
296A PRO* 3.7 8.3 - - + +
322A LEU* 4.2 22.9 - - + -
327A ARG* 3.6 40.6 - - + +
329A ASN 2.9 11.4 + - - +
330A ILE* 3.4 7.0 - - + +
331A LEU 2.9 23.6 + - - -
901B LEU* 3.4 40.8 - - + -
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Residues in contact with ILE 258 (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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241A ILE* 4.2 20.9 - - + -
245A LEU* 5.0 2.2 - - + -
256A VAL* 4.9 2.2 - - + -
257A VAL* 1.3 73.2 - - - +
259A LEU* 1.3 65.2 + - - +
260A PHE* 3.5 26.5 - - + -
288A MET* 4.2 21.8 - - + -
291A LEU* 4.6 3.6 - - + -
294A CYS* 5.2 1.1 - - - -
295A ASN* 3.8 30.3 - - + +
296A PRO 2.9 12.8 + - - +
297A TYR* 3.1 25.1 - - + +
298A ARG 3.1 6.1 + - - +
331A LEU* 3.5 16.8 - - + +
333A VAL* 3.7 24.2 - - + -
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Residues in contact with LEU 259 (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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257A VAL* 3.8 4.9 + - + -
258A ILE* 1.3 75.9 - - - +
260A PHE* 1.3 63.6 + - - +
261A SER* 3.5 2.3 + - - -
298A ARG* 3.5 28.9 - - + +
300A VAL* 4.1 21.8 - - + -
315A THR* 5.1 0.7 - - + -
318A SER* 4.3 11.2 - - - -
319A ILE* 3.9 26.9 - - + -
322A LEU* 3.7 33.7 - - + -
330A ILE* 4.0 11.4 - - + -
331A LEU 2.9 9.3 + - - -
332A LEU* 3.5 16.1 - - + +
333A VAL 2.9 23.9 + - - -
904B PRO* 4.9 4.3 - - + -
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Residues in contact with PHE 260 (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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241A ILE* 3.9 20.6 - - + -
258A ILE* 3.5 20.4 - - + -
259A LEU* 1.3 73.0 - - - +
261A SER* 1.3 59.6 + - - +
284A VAL* 3.6 38.8 - - + -
287A VAL* 4.0 14.6 - - + -
288A MET* 3.6 34.3 - - + -
297A TYR* 3.8 8.7 - + + -
298A ARG 2.9 16.6 + - - +
299A LEU* 3.5 7.1 - - + -
300A VAL* 2.8 29.8 + - - +
333A VAL* 3.3 15.9 - - + +
335A ILE* 3.8 30.5 - - + -
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Residues in contact with SER 261 (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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259A LEU 3.5 4.7 + - - -
260A PHE* 1.3 75.2 - - - +
262A ALA* 1.3 61.6 + - - +
300A VAL* 3.4 4.3 - - - -
302A GLN* 2.6 29.2 + - - +
315A THR* 2.7 36.3 + - - +
332A LEU* 5.7 1.8 - - - -
333A VAL 2.9 14.0 + - - -
334A PRO* 3.4 5.9 - - - +
335A ILE* 3.1 23.2 + - - -
336A ALA 4.3 0.5 + - - -
348A LEU* 4.9 7.9 - - - -
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Residues in contact with ALA 262 (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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261A SER* 1.3 75.5 + - - +
263A HIS* 1.3 67.3 + - - +
276A TYR* 3.5 14.4 - - - +
280A VAL* 4.0 12.6 - - + -
299A LEU* 4.7 0.4 - - + -
300A VAL 3.2 6.6 + - - +
301A TRP* 3.2 25.7 - - + +
302A GLN* 2.9 24.2 + - - -
335A ILE* 4.0 2.9 - - + -
336A ALA* 3.6 19.1 - - + +
343A GLU* 5.3 1.1 - - - -
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Residues in contact with HIS 263 (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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262A ALA* 1.3 72.5 - - - +
264A SER* 1.3 86.3 + - - +
276A TYR* 2.7 33.5 + - - -
301A TRP* 3.7 1.6 - - - -
302A GLN* 3.5 9.4 - - - -
303A SER* 3.4 27.4 - - - -
310A TRP* 4.0 8.7 - + - -
336A ALA* 4.8 1.8 - - + +
343A GLU* 3.2 32.9 + - + +
701A CHD 3.5 40.6 + - + +
1601A IMD 3.5 39.3 + + + +
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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