Contacts of the strand formed by residues 396 - 402 (chain A) in PDB entry 1H7B
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 SER 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A MET* 3.8 12.8 - - - +
292A SER* 4.5 1.7 + - - -
293A PHE 4.8 6.5 + - - -
294A LEU* 4.2 14.9 - - - +
295A SER 5.7 1.1 - - - -
309A ARG* 6.1 0.4 - - - -
310A ASN 2.9 7.5 + - - -
311A ASN* 3.0 24.9 + - - +
312A LEU* 2.8 30.7 + - - +
394A ARG 4.1 0.6 + - - -
395A SER* 1.3 74.9 - - - +
397A VAL* 1.3 58.9 + - - +
437A ALA* 3.4 14.1 - - - -
439A SER* 4.2 13.0 - - - -
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Residues in contact with VAL 397 (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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311A ASN* 3.9 1.6 - - - -
312A LEU* 3.8 19.5 - - + +
313A GLY 4.2 4.9 - - - +
352A LEU* 3.8 20.6 - - + -
356A ILE* 3.7 29.4 - - + -
395A SER 4.9 0.4 - - - +
396A SER* 1.3 77.8 - - - +
398A SER* 1.3 63.6 + - - +
436A PHE* 4.1 17.5 - - + -
437A ALA 3.3 5.0 + - - +
438A PHE* 3.4 33.8 - - + +
439A SER* 2.9 27.2 + - - +
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Residues in contact with SER 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A SER* 4.4 3.6 + - - -
311A ASN* 2.9 19.9 + - - -
313A GLY 2.9 17.6 + - - -
314A VAL* 3.4 16.6 - - - +
315A VAL 3.1 23.7 + - - -
352A LEU* 3.6 10.7 - - - +
396A SER* 4.9 0.3 + - - -
397A VAL* 1.3 72.8 - - - +
399A LEU* 1.3 59.1 + - - +
400A GLY 3.7 0.2 - - - -
438A PHE* 5.8 0.2 - - - -
439A SER* 3.7 6.7 + - - -
441A TYR* 3.7 30.5 - - - +
502A GLY 5.2 1.2 + - - -
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Residues in contact with LEU 399 (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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315A VAL 3.5 8.5 - - - +
317A LEU* 4.8 2.9 - - + -
345A MET* 3.5 35.0 - - + -
348A CYS* 3.5 37.9 - - + -
352A LEU* 4.5 6.0 - - + +
397A VAL 4.0 0.6 + - - -
398A SER* 1.3 70.7 - - - +
400A GLY* 1.3 69.3 - - - +
423A MET* 4.7 4.5 - - + -
427A LEU* 3.5 29.8 - - + -
430A TRP* 3.9 9.0 - - + -
438A PHE* 5.7 1.1 - - + -
439A SER 3.1 12.8 + - - +
440A LEU* 3.7 16.1 - - + +
441A TYR 3.0 19.5 + - - -
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Residues in contact with GLY 400 (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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314A VAL* 4.3 3.0 - - - +
315A VAL 2.7 14.4 + - - +
316A THR* 3.7 5.4 - - - -
317A LEU* 2.9 26.9 + - - +
398A SER 3.7 2.2 + - - -
399A LEU* 1.3 81.6 - - - +
401A TYR* 1.3 62.0 + - - +
423A MET* 5.8 0.2 - - - +
441A TYR* 3.1 16.8 - - - -
443A THR* 3.3 11.9 - - - -
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Residues in contact with TYR 401 (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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316A THR* 3.7 2.7 - - - -
317A LEU* 3.4 9.9 - - + +
319A LEU* 3.9 30.1 - - + -
400A GLY* 1.3 73.9 - - - +
402A ILE* 1.3 68.4 + - - +
404A ILE* 3.9 15.0 - - + -
420A LEU* 4.1 10.3 - - + +
423A MET* 4.2 12.3 - - + -
440A LEU* 3.8 25.4 - - + -
441A TYR 3.3 25.7 + - - -
442A SER* 2.8 20.7 + - - -
443A THR* 3.5 18.9 + - - -
475A SER* 3.5 29.9 + - - -
476A PHE* 3.1 18.7 - - - -
500A ALA* 3.5 12.7 - - + +
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Residues in contact with ILE 402 (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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316A THR* 4.2 3.8 - - + -
317A LEU 3.6 6.2 + - - +
318A ASN* 4.5 5.4 - - - +
319A LEU* 3.4 9.5 - - - +
320A PRO* 3.3 14.4 - - - +
401A TYR* 1.3 82.2 - - - +
403A GLY* 1.3 74.4 + - - +
404A ILE 3.7 1.8 - - - -
443A THR* 5.4 1.1 - - - +
445A ALA* 3.7 30.1 - - + -
448A LEU* 4.7 3.4 - - + +
449A CYS* 3.9 24.7 - - + +
452A PHE* 3.5 35.0 - - + -
472A TYR* 4.3 13.7 - - + +
473A THR 3.4 12.3 - - - +
474A ASN* 4.3 3.1 - - - -
475A SER* 4.0 13.5 - - - +
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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