Contacts of the strand formed by residues 459 - 467 (chain A) in PDB entry 1L7R
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 ASP 459 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A THR* 1.3 79.6 + - - +
460A PHE* 1.3 65.5 + - - +
480A ILE* 3.6 24.5 - - + +
481A VAL 3.3 6.1 - - - +
482A ARG* 2.8 47.3 + - - -
526A SER* 2.7 48.1 + - - +
527A SER* 5.5 0.9 - - - -
533A ASP 4.0 1.6 - - - +
535A ASN* 2.8 37.2 + - - +
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Residues in contact with PHE 460 (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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391A TYR* 3.4 26.7 - + - -
449A LEU* 5.0 2.2 - - + -
451A VAL* 3.5 38.6 - - + -
452A SER 3.9 9.6 - - - -
453A SER* 5.0 2.2 - - - -
458A THR* 3.6 17.0 - - + -
459A ASP* 1.3 78.8 - - - +
461A THR* 1.3 63.6 + - - +
480A ILE* 3.4 1.7 - - - +
481A VAL* 2.9 42.0 + - + -
483A MET* 3.8 18.4 - - + -
503A VAL* 5.3 0.9 - - + -
505A ILE* 3.5 12.5 - - + +
524A VAL* 5.0 0.9 - - + -
525A SER 3.2 4.5 - - - -
526A SER* 3.7 2.9 - - - -
555A ASN* 3.7 26.2 - - + -
556A ARG 4.5 1.3 - - - -
557A ILE* 3.8 26.7 - - + -
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Residues in contact with THR 461 (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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460A PHE* 1.3 77.0 - - - +
462A ALA* 1.3 62.9 + - - +
479A GLY 3.4 8.5 - - - +
480A ILE* 3.6 29.8 - - + -
505A ILE* 4.1 3.5 - - - +
523A GLN 4.3 1.1 + - - -
524A VAL* 3.3 12.5 - - - +
525A SER* 2.7 49.6 + - - -
526A SER 4.3 0.7 - - - -
527A SER 3.8 28.2 + - - +
528A ASN* 4.3 10.3 - - + +
532A TYR* 5.9 0.2 - - + -
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Residues in contact with ALA 462 (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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447A ALA* 4.3 8.5 - - + -
449A LEU* 5.0 1.8 - - + -
461A THR* 1.3 79.5 - - - +
463A LYS* 1.3 61.6 + - - +
478A ASP* 3.2 4.4 - - - +
479A GLY 3.0 30.4 + - - -
505A ILE* 4.0 18.4 - - + +
507A MET* 3.5 25.1 - - + +
522A VAL* 4.7 8.5 - - + -
523A GLN 3.2 7.4 - - - +
524A VAL* 4.8 4.5 - - + -
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Residues in contact with LYS 463 (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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399A VAL* 5.5 2.2 - - - +
400A PRO 5.2 1.8 + - - -
402A LEU 4.7 10.4 + - - +
418A GLN* 2.6 38.2 + - - +
421A ILE* 3.9 10.1 - - - +
462A ALA* 1.3 76.7 - - - +
464A LEU* 1.3 69.6 + - - +
465A VAL* 3.8 7.2 + - + +
475A ALA* 4.3 10.1 - - + -
477A CYS 3.5 10.8 - - - +
478A ASP* 3.8 17.0 - - + +
507A MET* 3.8 3.6 - - - -
521A MET 3.7 0.2 - - - +
522A VAL* 3.2 7.9 - - - +
523A GLN* 2.9 63.2 + - + +
528A ASN* 5.1 11.8 + - - +
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Residues in contact with LEU 464 (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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441A VAL* 4.5 4.5 - - + -
445A VAL* 4.6 3.1 - - + -
463A LYS* 1.3 72.7 - - - +
465A VAL* 1.3 63.4 + - - +
475A ALA* 3.8 0.7 - - - -
476A LEU* 2.9 48.1 + - + -
477A CYS* 2.8 36.4 + - - +
507A MET* 3.5 9.0 - - + +
510A THR* 4.3 11.2 - - + -
514A PHE* 4.3 7.9 - - + -
520A ILE* 3.9 24.5 - - + -
521A MET 3.6 13.2 - - - +
522A VAL* 4.2 3.4 - - + -
567A ILE* 4.0 16.8 - - + -
569A LEU* 4.1 18.6 - - + -
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Residues in contact with VAL 465 (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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418A GLN* 4.2 5.2 - - + -
463A LYS* 4.1 22.0 - - + +
464A LEU* 1.3 81.5 - - - +
466A ASP* 1.3 66.6 + - - +
467A VAL* 4.4 0.4 - - + -
473A ALA* 3.4 36.3 - - + +
474A ILE 3.4 12.1 - - - +
475A ALA* 4.3 2.5 - - - -
476A LEU* 4.3 1.6 - - - +
514A PHE* 3.6 11.0 - - - -
521A MET* 2.7 53.3 + - + +
523A GLN* 4.1 24.5 - - + +
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Residues in contact with ASP 466 (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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341A GLY* 5.3 2.3 - - - -
465A VAL* 1.3 71.9 - - - +
467A VAL* 1.3 63.2 + - - +
468A PHE* 3.5 20.9 - - + -
474A ILE* 2.9 36.9 + - + +
476A LEU* 4.1 7.1 - - + +
512A ASN* 3.0 26.7 + - - +
513A VAL 4.2 1.9 - - - +
514A PHE* 3.6 27.5 - - + -
518A HIS* 2.6 37.7 + - - +
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Residues in contact with VAL 467 (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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431A SER* 4.8 2.0 - - - +
465A VAL* 4.4 3.6 - - + -
466A ASP* 1.3 73.3 - - - +
468A PHE* 1.3 71.8 + - - +
471A GLY* 4.6 8.7 - - - +
472A ARG 3.5 7.9 - - - +
473A ALA* 4.2 5.8 - - + +
517A GLY 4.4 0.2 - - - +
518A HIS* 3.2 10.4 - - - +
519A ARG* 3.0 53.9 + - + +
521A MET* 3.7 42.4 - - + -
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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