Contacts of the strand formed by residues 472 - 479 (chain A) in PDB entry 4X7C
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 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A SER* 2.9 10.5 + - - -
471A ASP* 1.3 92.9 - - + +
473A ALA* 1.3 65.7 + - - +
490A LYS* 3.4 44.0 - - + +
491A LEU 3.5 3.8 - - - +
492A HIS* 3.9 26.7 - - + +
520A TRP* 3.6 4.2 - - - -
521A VAL* 2.9 50.5 + - + +
522A ASN* 5.0 4.3 - - - +
523A GLN* 6.4 1.3 - - + -
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Residues in contact with ALA 473 (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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227A PHE* 4.0 13.2 - - + -
268A THR* 5.7 0.7 - - + -
472A VAL* 1.3 74.0 - - - +
474A LEU* 1.3 63.5 + - - +
475A LEU* 3.4 2.1 + - + +
490A LYS* 3.7 1.4 - - - -
491A LEU* 2.7 51.4 + - + +
517A PHE* 3.3 28.7 - - + -
519A SER 3.7 3.6 - - - -
520A TRP* 3.9 16.2 - - + -
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Residues in contact with LEU 474 (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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472A VAL* 3.9 3.5 + - - +
473A ALA* 1.3 70.6 - - - +
475A LEU* 1.3 59.0 + - - +
476A ARG* 3.6 27.6 - - - +
488A GLU* 3.8 20.4 - - + +
489A CYS 3.7 15.9 - - - +
490A LYS* 5.1 1.8 - - + -
517A PHE* 3.7 4.0 - - - -
518A ASP* 2.9 26.3 + - + -
519A SER 2.7 21.3 + - - +
521A VAL* 3.8 14.1 - - + -
525A TYR* 3.7 35.2 - - + +
527A LEU* 3.9 11.4 - - + -
31C ILE* 4.0 22.9 - - + -
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Residues in contact with LEU 475 (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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229A VAL* 4.1 13.0 - - + -
457A TRP* 3.7 32.8 - - + -
473A ALA* 4.0 11.4 - - + +
474A LEU* 1.3 81.7 - - - +
476A ARG* 1.3 64.9 + - - +
488A GLU* 3.3 4.0 - - - +
489A CYS* 2.9 50.9 + - - -
491A LEU* 3.8 22.0 - - + -
497A VAL* 5.0 2.5 - - + -
515A PHE* 4.0 16.8 - - + -
516A ARG 3.3 6.1 - - - +
517A PHE* 3.8 29.6 - - + +
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Residues in contact with ARG 476 (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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474A LEU* 3.6 17.7 - - - +
475A LEU* 1.3 83.4 - - - +
477A PHE* 1.3 61.9 + - - +
478A VAL* 3.6 10.1 + - + +
485A VAL* 3.7 38.6 - - + +
487A PHE 3.6 1.8 - - - -
488A GLU* 3.1 32.1 + - + +
515A PHE* 3.5 2.1 - - - -
516A ARG* 2.8 34.7 + - - +
518A ASP* 2.8 45.2 + - - +
525A TYR* 3.5 12.1 + - - -
31C ILE* 3.9 19.8 - - - +
53C SER* 4.6 4.8 + - - -
54C GLY* 4.6 7.3 - - - -
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Residues in contact with PHE 477 (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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234A VAL* 4.2 5.8 - - + -
249A LEU* 4.2 5.8 - - + -
475A LEU 4.2 0.4 - - - -
476A ARG* 1.3 71.5 - - - +
478A VAL* 1.3 53.3 + - - +
485A VAL* 3.6 1.2 - - - -
486A LEU* 2.7 45.6 + - + +
487A PHE* 2.9 45.5 + + + +
488A GLU* 4.9 0.2 - - - +
489A CYS* 5.8 0.2 - - - -
509A ILE* 3.8 37.7 - - + -
510A PRO* 4.4 4.9 - - + -
513A GLY* 3.4 33.9 - - - -
514A TYR* 3.4 11.7 - - - -
515A PHE* 3.4 48.6 - + + +
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Residues in contact with VAL 478 (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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476A ARG 3.7 11.4 - - - +
477A PHE* 1.3 79.4 - - - +
479A ASN* 1.3 59.9 + - - +
480A PRO* 3.4 4.5 - - + +
483A GLY* 5.0 4.3 - - - +
484A ARG 3.4 8.1 - - - +
485A VAL* 3.9 12.8 - - + -
486A LEU* 4.6 2.5 - - - -
513A GLY* 3.2 6.1 - - - -
514A TYR* 2.8 75.9 + - + +
516A ARG* 3.7 39.0 - - + +
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Residues in contact with ASN 479 (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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478A VAL* 1.3 70.9 - - - +
480A PRO* 1.3 58.0 - - - +
481A ASP* 3.2 28.9 + - - +
482A THR* 3.2 23.6 + - - +
483A GLY* 2.6 36.1 + - - -
484A ARG* 2.8 15.8 + - + +
486A LEU* 3.9 9.9 - - + +
510A PRO* 3.6 34.4 - - + +
512A ASN* 4.5 0.7 - - - +
513A GLY* 4.5 2.0 - - - -
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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