Contacts of the strand formed by residues 251 - 258 (chain A) in PDB entry 3H1J
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 ALA 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A VAL* 1.3 75.0 - - - +
252A HIS* 1.3 63.9 + - - +
253A VAL* 5.1 1.7 - - + +
324A PHE* 3.6 2.4 - - - +
325A VAL* 3.3 4.5 - - - -
326A ALA* 2.9 33.7 + - - +
328A PRO 5.1 0.2 - - - -
331A ILE* 3.7 31.2 - - + -
425A VAL 3.2 13.9 - - - +
427A PRO* 3.7 14.6 - - + -
428A ILE* 3.8 7.2 - - + -
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Residues in contact with HIS 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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145A MET* 2.9 45.4 - - + +
146A THR* 3.6 18.0 + - - -
149A THR* 3.3 20.4 - - - +
250A VAL* 3.8 12.4 - - + +
251A ALA* 1.3 81.3 - - - +
253A VAL* 1.3 67.4 + - - +
323A HIS* 2.9 21.9 + - - +
324A PHE 3.5 3.1 - - - -
325A VAL* 3.2 28.9 - - + +
423A ALA 4.6 0.2 - - - -
424A ALA* 3.3 1.0 - - - -
425A VAL* 2.9 35.3 + - + +
428A ILE* 4.4 0.3 - - - +
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A THR* 4.6 0.2 - - - -
251A ALA 5.1 1.6 - - - -
252A HIS* 1.3 82.7 - - - +
254A ALA* 1.3 66.0 + - - +
322A PHE* 3.9 1.6 - - + +
323A HIS* 3.1 5.5 - - - -
324A PHE* 2.8 68.5 + - + -
331A ILE* 4.0 14.8 - - + -
335A MET* 3.4 33.2 - - + -
422A LEU* 4.0 10.5 - - + -
423A ALA 3.5 3.8 - - - -
424A ALA* 4.2 13.7 - - + -
428A ILE* 4.9 4.0 - - + -
431A LEU* 4.5 5.8 - - + -
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Residues in contact with ALA 254 (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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149A THR* 3.8 21.3 - - + +
150A PHE* 5.0 3.6 - - + -
153A LEU* 4.1 22.7 - - + +
253A VAL* 1.3 77.6 - - - +
255A LEU* 1.3 60.7 + - - +
310A PHE* 4.9 2.0 - - + -
322A PHE 3.2 9.9 - - - +
323A HIS* 4.2 9.6 - - + -
421A ALA 3.7 0.7 - - - +
422A LEU* 3.5 5.6 - - - +
423A ALA* 3.0 34.5 + - + +
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Residues in contact with LEU 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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153A LEU* 5.0 0.4 - - - -
254A ALA* 1.3 74.6 - - - +
256A ALA* 1.3 63.9 + - - +
310A PHE* 4.2 0.6 - - - -
321A GLY* 3.0 2.3 - - - -
322A PHE* 3.0 58.2 + - + -
335A MET* 4.5 8.1 - - + -
339A GLN* 4.4 17.5 - - - +
342A TRP* 3.7 27.0 - - + -
420A PRO* 3.4 33.7 - - + -
421A ALA 3.2 9.9 - - - +
422A LEU* 4.0 23.6 - - + -
437A ILE* 4.3 9.0 - - + -
441A MET* 4.7 1.8 - - - -
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Residues in contact with ALA 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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153A LEU* 4.2 14.8 - - + -
236A PHE* 3.6 3.8 - - - -
255A LEU* 1.3 78.6 - - - +
257A VAL* 1.3 65.7 + - - +
310A PHE* 4.2 11.4 - - + -
319A LEU* 4.4 10.1 - - + -
320A PHE 3.2 25.4 - - - +
321A GLY* 3.7 2.5 - - - +
342A TRP* 4.2 3.1 - - - -
420A PRO* 3.4 5.2 - - - +
421A ALA* 2.8 36.9 + - + -
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Residues in contact with VAL 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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236A PHE* 3.8 10.1 - - + -
256A ALA* 1.3 79.0 - - - +
258A GLU* 1.3 64.7 + - - +
319A LEU* 3.6 2.8 - - - -
320A PHE* 2.8 59.0 + - + +
342A TRP* 4.3 8.7 - - + -
414A TYR* 3.4 31.4 - - + +
415A ILE* 4.7 3.6 - - + -
418A LYS* 4.3 10.8 - - + -
419A CYS 5.2 0.7 - - - +
420A PRO* 4.6 5.2 - - + -
441A MET* 4.1 26.0 - - + -
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Residues in contact with GLU 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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233A ARG* 4.0 16.9 + - - -
234A CYS 5.1 1.6 - - - -
236A PHE* 2.8 52.0 + - + +
257A VAL* 1.3 78.6 - - - +
259A GLY* 1.3 64.6 + - - +
316A ASP 4.8 1.0 - - - +
317A THR* 3.1 30.3 + - - +
318A GLY 3.4 5.4 - - - +
414A TYR* 3.7 17.0 - - - +
24E SER* 4.3 8.8 + - - -
25E SER* 4.7 1.7 + - - -
26E GLN* 3.2 38.6 + - - +
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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