Contacts of the strand formed by residues 513 - 521 (chain A) in PDB entry 1Q57
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 LEU 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504A ARG* 4.0 16.2 - - - +
505A ASN 4.4 2.3 + - - -
510A MET* 2.8 67.4 + - + +
512A ASN* 1.3 78.0 - - - +
514A VAL* 1.3 61.7 + - - +
532A TYR* 3.7 35.0 - - + -
533A MET 3.2 20.2 - - - +
534A GLU* 4.6 7.4 - - + +
545A SER* 4.6 10.8 - - - +
547A TYR* 3.5 15.3 - - + -
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Residues in contact with VAL 514 (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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317A VAL* 4.2 22.4 - - + -
502A LEU* 4.0 20.2 - - + -
503A GLU 3.1 13.7 - - - +
504A ARG* 4.2 9.4 - - + +
512A ASN 3.8 9.4 - - - +
513A LEU* 1.3 80.4 - - - +
515A LEU* 1.3 72.0 + - - +
516A VAL* 5.1 0.4 - - + -
532A TYR* 3.4 4.6 - - - -
533A MET* 2.9 60.8 + - + +
535A TYR* 4.7 0.7 - - + +
542A LEU* 4.2 14.4 - - + -
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Residues in contact with LEU 515 (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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502A LEU* 3.2 6.6 - - - -
503A GLU* 2.8 61.5 + - + +
513A LEU* 4.4 0.6 + - - +
514A VAL* 1.3 76.7 - - - +
516A VAL* 1.3 63.4 + - - +
517A ARG* 3.5 21.5 - - - +
529A ILE* 3.1 34.5 - - + -
531A GLY 3.9 4.5 - - - +
532A TYR* 3.4 39.5 - - + +
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Residues in contact with VAL 516 (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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292A CYS* 4.3 3.8 - - - -
295A ILE* 3.5 27.4 - - + -
321A PHE* 5.5 0.9 - - + -
500A ILE* 3.3 25.8 - - + -
501A ALA 3.3 14.6 - - - +
502A LEU* 4.5 9.2 - - + -
514A VAL* 4.3 7.0 - - + +
515A LEU* 1.3 81.5 - - - +
517A ARG* 1.3 56.9 + - - +
518A ILE* 5.6 0.2 - - + -
529A ILE* 3.6 1.7 - - - -
530A ALA* 2.8 33.0 + - + +
531A GLY 3.1 25.1 + - - +
533A MET* 4.3 17.3 - - + -
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Residues in contact with ARG 517 (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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480A PRO* 3.6 19.9 - - - +
481A VAL* 3.6 19.5 - - - +
500A ILE* 3.6 4.9 - - - +
501A ALA* 2.9 36.9 + - + +
503A GLU* 2.8 41.9 + - - +
515A LEU* 3.5 11.3 - - - +
516A VAL* 1.3 73.4 - - - +
518A ILE* 1.3 62.8 + - - +
519A LEU* 3.1 19.5 + - + -
528A GLY* 3.5 5.5 - - - -
529A ILE* 3.2 39.3 - - + +
476B GLU* 5.6 8.9 + - - +
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Residues in contact with ILE 518 (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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295A ILE* 4.5 5.8 - - + -
298A LYS* 4.1 14.6 - - + -
299A THR* 3.5 24.2 - - + -
498A THR* 4.3 0.9 - - + -
499A ILE 4.0 1.8 - - - +
500A ILE* 3.5 35.2 - - + -
516A VAL* 3.9 0.6 + - + -
517A ARG* 1.3 72.6 - - - +
519A LEU* 1.3 64.1 + - - +
520A LYS 3.4 23.8 - - - +
521A CYS* 4.2 4.9 - - + -
526A ASP 4.0 6.1 - - - +
527A THR* 3.3 21.5 - - - -
528A GLY* 2.6 42.2 + - - +
530A ALA* 4.1 11.9 - - + -
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Residues in contact with LEU 519 (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 THR* 5.2 1.8 - - + -
481A VAL* 3.3 40.8 - - + +
482A SER 3.7 14.8 - - - +
483A ILE* 3.7 34.3 - - + +
486A LEU* 5.8 3.4 - - + -
499A ILE* 2.6 35.2 + - + +
501A ALA* 4.1 7.9 - - + -
517A ARG* 3.1 40.6 + - + +
518A ILE* 1.3 74.5 - - - +
520A LYS* 1.3 66.5 + - - +
527A THR* 4.6 4.0 - - - +
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Residues in contact with LYS 520 (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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483A ILE* 5.4 4.3 - - + -
492A LEU 4.8 0.4 + - - -
493A ARG 3.6 17.2 + - - +
494A GLN* 2.8 27.9 + - - +
496A SER* 2.6 22.6 + - - -
497A ASP* 3.4 12.1 - - - +
498A THR* 3.1 6.2 - - - +
499A ILE* 2.8 40.8 + - + +
518A ILE* 3.2 6.0 - - - +
519A LEU* 1.3 86.3 - - - +
521A CYS* 1.3 68.7 + - - +
522A ARG* 4.8 12.3 - - + +
527A THR* 3.9 10.5 - - - -
343B GLU* 5.2 12.1 + - - +
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Residues in contact with CYS 521 (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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298A LYS 3.9 0.2 - - - -
299A THR* 3.5 28.0 - - - -
303A ARG* 4.3 4.3 - - - -
497A ASP 3.3 5.8 - - - -
498A THR* 3.9 13.2 - - + -
518A ILE* 4.2 10.8 - - + -
520A LYS* 1.3 83.4 - - - +
522A ARG* 1.3 58.8 + - - +
523A PHE 3.4 0.7 - - - -
524A THR* 3.0 32.3 + - - -
525A GLY* 2.3 43.6 + - - +
526A ASP 4.2 5.4 - - - +
527A THR* 4.3 3.8 - - + +
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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