Contacts of the strand formed by residues 456 - 463 (chain B) in PDB entry 3H7W
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 TYR 456 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A THR* 4.2 15.1 + - - +
245A LEU* 5.5 2.5 - - + +
260A ARG* 5.5 1.9 + - - -
340A VAL* 4.6 1.6 - - + +
366B ARG* 3.4 41.3 + - + -
367B HIS 3.3 14.8 - - - +
368B ASN* 4.8 3.6 - - - +
369B ILE* 5.0 2.0 - - - -
374B THR* 5.7 0.2 - - - +
445B THR* 3.3 5.4 - - - -
446B PHE* 2.9 68.2 + + + -
447B GLN* 5.1 2.7 - - - -
448B ASN 5.8 0.2 - - - -
454B ILE* 4.2 10.3 - - + +
455B GLU* 1.3 74.8 - - - +
457B ILE* 1.3 64.5 + - - +
458B ILE* 3.7 22.0 - - + -
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Residues in contact with ILE 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B SER 4.0 0.2 - - - +
366B ARG* 3.2 6.1 - - - +
367B HIS* 2.8 42.5 + - + +
368B ASN 4.0 10.5 - - - +
369B ILE* 4.1 11.9 - - + -
412B PHE* 3.6 36.1 - - + +
415B VAL* 3.6 27.4 - - + -
416B VAL* 4.4 5.2 - - + -
443B SER* 3.9 14.4 - - - -
444B PHE 3.5 7.9 - - - +
445B THR* 4.1 9.2 - - + -
456B TYR* 1.3 80.0 - - - +
458B ILE* 1.3 62.8 + - - +
459B CYS* 3.9 22.2 + - - -
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Residues in contact with ILE 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 3.9 29.2 - - + -
338A MET* 4.1 21.8 - - + -
340A VAL* 4.5 8.7 - - + -
364B ILE* 4.8 2.9 - - + -
365B SER 3.7 3.4 - - - +
366B ARG* 4.1 10.5 - - + -
442B SER 3.8 0.9 - - - +
443B SER* 3.2 3.6 - - - -
444B PHE* 2.9 72.2 + - + +
446B PHE* 4.6 4.5 - - + -
456B TYR* 3.7 32.1 - - + -
457B ILE* 1.3 76.5 - - - +
459B CYS* 1.3 66.1 + - - +
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Residues in contact with CYS 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B ILE* 3.3 8.3 - - - +
365B SER* 2.9 46.1 + - - +
367B HIS* 3.6 23.6 - - - -
396B ILE* 5.2 0.4 - - - -
412B PHE* 3.9 14.4 - - - -
441B THR* 3.7 19.3 - - + -
442B SER 3.3 4.3 - - - -
443B SER* 3.8 13.0 - - - -
457B ILE* 3.9 4.3 - - - -
458B ILE* 1.3 78.6 - - - +
460B THR* 1.3 61.7 + - - +
461B ASN* 3.6 12.8 - - - +
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Residues in contact with THR 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLU* 4.4 7.2 - - - +
326A ILE* 4.2 17.2 - - + +
335A GLN* 5.1 0.2 - - - +
336A CYS* 4.8 7.6 - - - -
338A MET* 3.3 33.6 - - - +
362B ARG* 3.7 30.5 - - - -
363B PHE 3.8 6.5 - - - +
364B ILE* 4.2 2.6 - - + +
440B ARG 3.5 2.3 - - - +
441B THR* 3.3 2.6 - - - -
442B SER* 2.9 35.5 + - - -
444B PHE* 5.7 1.1 - - - -
458B ILE* 5.6 0.2 - - - +
459B CYS* 1.3 75.0 + - - +
461B ASN* 1.3 60.6 + - - +
462B THR* 4.1 6.5 + - - +
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Residues in contact with ASN 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B ARG* 3.1 4.2 - - - -
363B PHE* 2.9 68.2 + - + +
365B SER* 2.9 29.1 + - - +
373B PHE* 5.2 1.2 - - - -
383B THR* 4.3 0.2 - - - +
396B ILE* 4.6 7.7 - - - +
427B PHE* 6.2 0.2 - - - -
429B PHE* 6.2 2.0 - - + -
439B MET* 3.5 21.1 - - + +
440B ARG 3.6 4.5 - - - -
441B THR* 2.7 36.3 + - - +
459B CYS* 3.6 4.4 - - - +
460B THR* 1.3 73.9 - - - +
462B THR* 1.3 57.1 + - - +
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Residues in contact with THR 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ILE* 5.9 0.9 - - - +
335A GLN* 2.9 31.4 + - - +
360B PRO* 3.7 16.6 - - + -
361B THR 3.4 12.8 - - - +
362B ARG* 3.4 10.9 - - + +
439B MET* 3.3 5.7 - - - +
440B ARG* 2.9 38.7 + - - -
460B THR* 4.3 6.1 + - - +
461B ASN* 1.3 72.8 - - - +
463B ASN* 1.3 76.2 + - - +
464B VAL* 3.4 14.4 + - + +
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Residues in contact with ASN 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B PRO* 5.2 1.9 - - - +
361B THR* 3.0 25.1 + - - +
383B THR* 4.4 10.9 - - + +
437B LEU* 3.9 29.5 - - - +
438B TRP 2.8 37.6 + - - +
439B MET* 3.7 11.7 - - - +
462B THR* 1.3 79.0 - - - +
464B VAL* 1.3 65.5 + - - +
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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