Contacts of the strand formed by residues 513 - 521 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504D ARG* 4.0 16.9 - - - +
505D ASN 4.4 2.3 + - - -
510D MET* 2.8 65.2 + - + +
512D ASN* 1.3 76.8 - - - +
514D VAL* 1.3 62.6 + - - +
515D LEU 4.4 0.2 + - - -
532D TYR* 3.6 36.1 - - + -
533D MET 3.2 19.7 - - - +
534D GLU* 4.6 8.5 - - + +
545D SER* 4.6 9.6 - - - +
547D TYR* 3.4 19.1 - - + +
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Residues in contact with VAL 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D VAL* 4.0 27.8 - - + -
502D LEU* 4.0 19.5 - - + -
503D GLU 3.2 13.5 - - - +
504D ARG* 4.3 6.1 - - + +
512D ASN 3.8 9.4 - - - +
513D LEU* 1.3 80.3 - - - +
515D LEU* 1.3 71.6 + - - +
516D VAL* 5.1 0.4 - - + -
532D TYR* 3.4 4.3 - - - -
533D MET* 2.8 60.1 + - + +
535D TYR* 4.6 1.3 - - + +
542D LEU* 4.3 11.4 - - + -
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Residues in contact with LEU 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502D LEU* 3.1 6.8 - - - +
503D GLU* 2.8 59.2 + - + +
513D LEU* 5.3 0.2 - - - +
514D VAL* 1.3 77.3 - - - +
516D VAL* 1.3 64.1 + - - +
517D ARG* 3.5 21.5 - - - +
529D ILE* 3.0 34.8 - - + -
531D GLY 3.9 5.2 - - - +
532D TYR* 3.4 40.6 - - + +
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Residues in contact with VAL 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D CYS* 4.2 4.5 - - - -
295D ILE* 3.4 29.2 - - + -
321D PHE* 5.5 0.7 - - + -
500D ILE* 3.4 24.5 - - + -
501D ALA 3.3 13.9 - - - +
502D LEU* 4.6 8.7 - - + -
514D VAL* 4.3 1.1 - - + +
515D LEU* 1.3 82.3 - - - +
517D ARG* 1.3 61.6 + - - +
518D ILE* 5.6 0.4 - - + -
529D ILE* 3.6 1.7 - - - +
530D ALA* 2.8 30.1 + - + +
531D GLY 3.1 24.0 + - - +
533D MET* 4.3 22.7 - - + -
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Residues in contact with ARG 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D PRO* 3.7 20.1 - - - +
481D VAL* 3.5 19.7 - - - -
500D ILE* 3.6 5.2 - - - +
501D ALA* 2.8 37.0 + - + +
503D GLU* 2.8 41.1 + - - +
515D LEU* 3.5 10.9 - - + +
516D VAL* 1.3 72.7 - - - +
518D ILE* 1.3 60.8 + - - +
519D LEU* 3.1 19.3 - - + -
528D GLY* 3.6 7.1 - - - -
529D ILE* 3.3 38.7 - - + +
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Residues in contact with ILE 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D ILE* 4.5 7.0 - - + +
298D LYS* 4.2 7.9 - - + -
299D THR* 3.5 28.7 - - + -
498D THR* 4.3 1.1 - - + -
499D ILE 4.1 1.8 - - - +
500D ILE* 3.6 30.1 - - + -
516D VAL* 3.9 0.4 + - + -
517D ARG* 1.3 72.8 - - - +
519D LEU* 1.3 65.9 + - - +
520D LYS 3.4 24.7 - - - +
521D CYS* 4.1 5.2 - - + -
526D ASP 4.0 6.7 - - - +
527D THR* 3.3 18.4 - - - -
528D GLY* 2.7 37.0 + - - +
530D ALA* 4.2 17.7 - - + -
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Residues in contact with LEU 519 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314C SER* 5.4 2.3 + - - -
311D THR* 5.1 2.2 - - + -
481D VAL* 3.4 39.7 - - + +
482D SER* 3.8 14.6 - - - +
483D ILE* 3.7 34.3 - - + +
486D LEU* 5.8 3.6 - - + -
499D ILE* 2.6 35.8 + - + -
501D ALA* 4.2 8.5 - - + -
517D ARG* 3.1 40.6 + - + -
518D ILE* 1.3 75.3 - - - +
520D LYS* 1.3 65.8 + - - +
527D THR* 4.7 3.8 - - - +
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Residues in contact with LYS 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C SER* 5.3 10.5 - - - +
343C GLU* 5.4 1.8 + - - -
483D ILE* 5.3 4.9 - - + -
492D LEU 4.8 0.2 + - - -
493D ARG 3.6 16.2 + - - +
494D GLN* 2.8 28.5 + - - +
496D SER* 2.7 22.4 + - - -
497D ASP* 3.4 11.7 - - - +
498D THR* 3.2 6.2 - - - +
499D ILE* 2.8 39.4 + - + +
518D ILE* 3.1 6.9 + - - +
519D LEU* 1.3 86.1 - - - +
521D CYS* 1.3 68.2 + - - +
522D ARG* 4.9 13.2 - - + +
527D THR* 4.0 10.5 - - - -
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Residues in contact with CYS 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D LYS 3.9 0.2 - - - -
299D THR* 3.5 28.3 - - - -
303D ARG* 4.4 3.8 - - - -
497D ASP 3.4 5.4 - - - -
498D THR* 4.1 10.3 - - + +
518D ILE* 4.1 5.8 - - + -
520D LYS* 1.3 82.1 - - - +
522D ARG* 1.3 60.2 + - - +
523D PHE 4.6 0.4 - - - -
524D THR* 3.3 35.4 - - - +
525D GLY* 2.3 44.6 + - - +
526D ASP 4.1 11.4 - - - +
527D 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