Contacts of the strand formed by residues 254 - 259 (chain A) in PDB entry 1HJV
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 LEU 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A ILE* 3.6 22.9 - - + +
203A ILE* 4.8 11.7 - - + -
241A VAL* 3.9 28.3 - - + +
244A MET* 4.2 16.2 - - + -
245A LEU* 4.0 14.4 - - + +
249A ALA* 4.0 22.7 - - + -
250A PRO 3.2 5.8 + - - +
251A ALA* 3.0 12.7 + - - +
252A SER 3.5 0.6 - - - -
253A LYS* 1.3 79.1 - - - +
255A VAL* 1.3 62.4 + - - +
256A MET 4.0 0.2 - - - -
346A LEU* 3.5 31.9 - - + +
347A ALA* 2.9 26.1 + - - +
348A GLY 3.6 0.3 + - - -
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Residues in contact with VAL 255 (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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23A LYS* 4.7 7.4 - - + +
25A VAL* 4.2 11.9 - - + -
200A PHE* 3.7 35.9 - - + -
201A ILE 2.7 10.9 + - - +
202A SER* 3.5 11.1 - - - +
203A ILE* 2.9 32.7 + - - +
254A LEU* 1.3 77.4 - - - +
256A MET* 1.3 59.0 + - - +
257A GLY 3.3 0.3 + - - -
347A ALA* 4.4 9.2 - - + -
348A GLY* 3.5 5.2 - - - +
349A ALA* 3.3 10.8 - - - +
350A MET* 3.2 39.0 - - + +
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Residues in contact with MET 256 (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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203A ILE* 3.9 5.2 - - + -
205A THR* 3.8 11.4 - - - +
222A LEU* 4.8 0.2 - - + -
237A THR* 3.4 28.0 - - + -
241A VAL* 4.0 14.1 - - + -
254A LEU 3.9 1.4 + - - -
255A VAL* 1.3 71.4 - - - +
257A GLY* 1.3 65.5 + - - +
258A ILE* 3.4 16.3 + - + +
337A LYS* 3.5 46.0 - - + +
340A TYR* 3.9 19.7 - - + -
341A LEU* 4.1 12.8 - - + -
346A LEU* 4.2 10.8 - - + -
348A GLY 2.8 18.3 + - - +
349A ALA* 3.3 7.8 - - - +
350A MET 2.8 19.5 + - - +
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Residues in contact with GLY 257 (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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203A ILE 2.8 27.3 + - - -
205A THR* 2.5 29.6 + - - +
206A TYR* 4.4 6.1 - - - -
237A THR* 5.2 0.3 - - - +
255A VAL 3.3 2.2 + - - -
256A MET* 1.3 75.1 - - - +
258A ILE* 1.3 61.8 + - - +
259A PRO 4.3 0.2 - - - -
337A LYS* 5.5 1.7 + - - +
350A MET* 3.4 23.8 - - - -
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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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206A TYR* 4.3 3.4 - - - -
256A MET* 3.7 19.3 - - + +
257A GLY* 1.3 77.8 - - - +
259A PRO* 1.3 75.1 - - + +
260A THR* 4.0 1.5 + - + -
329A ASP* 4.8 3.6 - - - +
334A VAL* 3.7 33.0 - - + +
337A LYS* 4.0 26.7 - - + -
338A VAL* 4.5 4.0 - - + -
341A LEU* 5.0 0.4 - - + -
349A ALA* 4.1 15.3 - - + -
350A MET 2.7 13.0 + - - +
351A VAL* 3.3 7.1 - - - +
352A TRP 3.1 21.0 + - - -
376A ILE* 3.8 26.5 - - + -
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Residues in contact with PRO 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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206A TYR* 3.6 18.5 - - + -
219A HIS* 3.7 15.7 - - + +
220A SER* 3.7 21.1 - - - +
257A GLY 4.4 0.9 - - - +
258A ILE* 1.3 99.4 - - + +
260A THR* 1.3 60.4 + - - +
261A PHE* 3.4 27.3 + - + +
329A ASP* 3.7 32.4 - - + +
334A VAL* 5.2 0.3 - - - +
337A LYS* 4.2 2.0 - - - +
352A TRP 3.5 7.6 - - - +
372A LEU* 5.0 0.3 - - - +
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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