Contacts of the strand formed by residues 397 - 407 (chain A) in PDB entry 4EG8
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 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A TRP* 3.7 20.2 - - + -
363A TYR 3.4 12.3 - - - +
364A SER* 4.1 4.7 - - - -
371A LEU* 3.7 26.7 - - + -
376A ILE* 4.2 9.4 - - + -
387A CYS* 5.9 0.3 - - - +
388A LYS* 3.1 41.6 + - + +
389A VAL 3.6 3.8 - - - +
390A SER* 3.6 22.4 - - - +
395A HIS 3.7 1.6 - - - +
396A VAL* 1.3 81.9 - - - +
398A THR* 1.3 67.3 + - - +
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Residues in contact with THR 398 (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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362A TRP* 3.6 6.6 - - - -
363A TYR* 2.8 40.0 + - - +
365A ILE* 4.0 25.3 + - + +
396A VAL* 4.8 10.4 + - + +
397A VAL* 1.3 80.0 - - - +
399A TRP* 1.3 66.6 + - - +
400A VAL* 3.7 5.9 + - - +
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Residues in contact with TRP 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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360A GLU* 3.7 18.7 + - + +
361A GLY* 3.5 43.3 - - - -
362A TRP* 3.6 48.1 - + + -
373A PRO* 5.8 4.0 - - + -
398A THR* 1.3 75.9 - - - +
400A VAL* 1.3 73.1 + - - +
401A SER* 4.2 13.7 + - - -
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Residues in contact with VAL 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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359A TYR* 3.3 19.7 - - + +
360A GLU* 3.3 4.2 - - - -
361A GLY 2.8 35.9 + - - +
363A TYR* 3.8 25.1 - - + -
370A PHE* 5.5 0.4 - - + -
398A THR* 4.3 6.5 - - - +
399A TRP* 1.3 79.5 + - - +
401A SER* 1.3 63.5 + - - +
402A GLU* 4.0 20.2 - - + +
404A ASN* 5.2 0.7 - - - +
451A ARG* 3.5 36.8 - - - +
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Residues in contact with SER 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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358A ARG* 3.1 22.5 + - - -
359A TYR 3.4 4.3 - - - -
360A GLU* 3.4 17.5 + - - +
399A TRP* 4.2 17.6 + - - -
400A VAL* 1.3 76.1 - - - +
402A GLU* 1.3 64.3 + - - +
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Residues in contact with GLU 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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358A ARG* 3.3 9.2 - - - +
359A TYR 3.0 30.5 + - - -
400A VAL* 4.0 9.7 - - + +
401A SER* 1.3 78.2 + - - +
403A GLU* 1.3 62.5 + - - +
404A ASN* 3.1 15.4 + - - +
451A ARG* 2.9 38.9 + - - -
452A ALA* 2.9 31.9 + - + -
455A THR* 3.0 25.5 + - - +
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Residues in contact with GLU 403 (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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356A LEU* 3.7 34.6 - - + +
357A GLY 3.3 16.7 - - - +
358A ARG* 3.6 24.6 + - + +
402A GLU* 1.3 71.8 - - - +
404A ASN* 1.3 67.3 + - - +
452A ALA* 4.9 3.5 + - - +
469A HIS* 3.4 18.5 + - + +
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Residues in contact with ASN 404 (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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356A LEU* 4.3 5.2 - - - -
357A GLY 2.9 33.3 + - - +
359A TYR* 4.0 10.9 - - - +
370A PHE* 4.9 0.5 - - - -
400A VAL* 5.2 0.7 - - - +
402A GLU* 3.1 36.6 + - - +
403A GLU* 1.3 85.1 + - - +
405A TYR* 1.3 63.4 + - - +
406A MET* 3.5 7.7 + - - +
448A SER* 2.6 32.0 + - - +
450A SER* 2.9 19.0 + - - +
451A ARG* 3.5 15.4 + - - +
452A ALA 4.1 0.4 - - - +
469A HIS* 4.0 1.1 - - - -
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Residues in contact with TYR 405 (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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345A TRP* 3.7 26.5 - + + -
354A ILE* 3.9 19.1 - - + -
355A TYR* 3.4 11.4 - - - -
356A LEU* 3.7 29.0 - - + +
404A ASN* 1.3 71.7 - - - +
406A MET* 1.3 59.4 + - - +
448A SER* 3.5 3.6 - - - -
449A VAL* 2.8 25.9 + - - -
450A SER* 2.7 26.2 + - - +
463A VAL* 4.4 3.1 - - + -
466A ASN* 2.7 42.5 + - + +
469A HIS* 3.5 17.9 - + + -
801A GOL 4.0 26.7 + - - -
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Residues in contact with MET 406 (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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354A ILE* 3.3 5.4 - - - -
355A TYR* 2.7 72.7 + - + +
357A GLY* 4.0 8.1 - - - -
358A ARG 4.0 24.7 - - - +
359A TYR* 4.5 8.1 - - + -
404A ASN* 3.7 14.4 - - - +
405A TYR* 1.3 74.3 - - - +
407A PHE* 1.3 61.0 + - - +
446A ASP* 3.8 26.0 - - + +
447A LEU 3.4 1.6 - - - -
448A SER* 3.6 34.5 - - - +
449A VAL* 4.0 3.6 - - - -
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Residues in contact with PHE 407 (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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348A LEU* 4.3 12.1 - - + -
353A ASP* 3.3 33.0 - - + -
354A ILE* 4.3 3.8 - - + -
355A TYR* 4.8 0.2 - - - -
406A MET* 1.3 72.6 - - - +
408A ARG* 1.3 58.5 + - - +
409A LEU* 2.9 32.9 + - + -
412A PHE* 3.5 20.6 - + - -
446A ASP* 3.2 7.9 - - - +
447A LEU* 2.7 34.2 + - + +
449A VAL* 3.6 27.8 - - + +
529A ALA* 3.7 36.6 - - + -
530A PHE* 3.6 29.2 - + - -
533A SER* 3.9 11.0 - - - -
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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