Contacts of the strand formed by residues 513 - 521 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504E ARG* 4.0 16.9 - - - +
505E ASN 4.4 2.4 + - - -
510E MET* 2.9 62.1 + - + +
512E ASN* 1.3 79.0 - - - +
514E VAL* 1.3 61.3 + - - +
532E TYR* 3.6 34.5 - - + -
533E MET 3.1 20.4 - - - +
534E GLU* 4.6 7.6 - - + +
545E SER* 4.6 11.2 - - - +
547E TYR* 3.6 15.9 - - + -
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Residues in contact with VAL 514 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E VAL* 3.9 27.6 - - + -
502E LEU* 3.9 20.4 - - + -
503E GLU 3.2 15.5 - - - +
504E ARG* 4.3 5.6 - - + +
512E ASN 3.8 8.1 - - - +
513E LEU* 1.3 80.5 - - - +
515E LEU* 1.3 70.8 + - - +
516E VAL* 4.2 1.6 - - + +
532E TYR* 3.4 5.2 - - - -
533E MET* 2.9 58.6 + - + +
535E TYR* 4.7 1.1 - - + +
542E LEU* 4.1 13.5 - - + -
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Residues in contact with LEU 515 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502E LEU* 3.1 5.9 - - - -
503E GLU* 2.8 61.2 + - + +
514E VAL* 1.3 75.1 - - - +
516E VAL* 1.3 65.1 + - - +
517E ARG* 3.5 20.9 - - - +
529E ILE* 3.0 35.7 - - + -
531E GLY 3.9 4.9 - - - +
532E TYR* 3.4 39.7 - - + +
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Residues in contact with VAL 516 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292E CYS* 4.3 4.3 - - - -
295E ILE* 3.4 33.7 - - + -
321E PHE* 5.6 0.4 - - + -
500E ILE* 3.5 27.6 - - + -
501E ALA 3.3 5.6 - - - +
502E LEU* 4.6 8.1 - - + -
514E VAL* 4.2 7.4 - - + +
515E LEU* 1.3 83.5 - - - +
517E ARG* 1.3 59.9 + - - +
518E ILE* 5.6 0.4 - - + -
529E ILE* 3.6 1.7 - - - +
530E ALA* 2.8 29.2 + - + +
531E GLY 3.1 25.7 + - - +
533E MET* 4.3 16.8 - - + -
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Residues in contact with ARG 517 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507D GLN* 5.8 4.6 + - - +
480E PRO* 3.7 18.6 - - - +
481E VAL 3.6 19.3 - - - -
500E ILE* 3.6 4.9 - - - +
501E ALA* 2.9 37.7 + - + +
503E GLU* 2.7 37.4 + - - +
515E LEU* 3.5 14.5 - - + +
516E VAL* 1.3 72.9 - - - +
518E ILE* 1.3 61.8 + - - +
519E LEU* 3.3 19.5 + - + -
528E GLY* 3.5 6.2 - - - -
529E ILE* 3.1 39.4 - - + +
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Residues in contact with ILE 518 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295E ILE* 4.5 6.7 - - + -
298E LYS* 4.1 6.7 - - + -
299E THR* 3.5 25.4 - - + -
498E THR* 4.3 0.9 - - + -
499E ILE 4.0 2.2 - - - +
500E ILE* 3.5 33.9 - - + -
516E VAL 3.9 0.2 + - - -
517E ARG* 1.3 73.2 - - - +
519E LEU* 1.3 65.1 + - - +
520E LYS 3.5 21.3 - - - +
521E CYS* 4.2 5.4 - - + -
526E ASP 4.0 4.9 - - - +
527E THR* 3.3 23.3 - - + -
528E GLY* 2.7 43.2 + - - +
530E ALA* 4.1 17.9 - - + -
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Residues in contact with LEU 519 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E THR* 5.1 2.7 - - + -
481E VAL* 3.5 35.9 - - + +
482E SER* 3.7 18.6 - - - +
483E ILE* 3.6 33.4 - - + +
486E LEU* 5.8 3.6 - - + -
499E ILE* 2.7 36.3 + - + -
501E ALA* 4.0 8.5 - - + -
517E ARG* 3.3 35.6 + - + -
518E ILE* 1.3 73.3 - - - +
520E LYS* 1.3 63.8 + - - +
527E THR* 4.6 3.6 - - - +
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Residues in contact with LYS 520 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483E ILE* 5.4 3.8 - - + -
492E LEU 4.7 0.6 + - - -
493E ARG 3.8 14.6 + - - +
494E GLN* 2.8 30.3 + - - +
496E SER* 2.7 22.1 + - - -
497E ASP* 3.3 12.3 - - - +
498E THR* 3.0 8.8 - - - +
499E ILE* 2.7 44.7 + - + +
518E ILE* 3.2 5.6 - - - +
519E LEU* 1.3 84.6 - - - +
521E CYS* 1.3 63.7 + - - +
522E ARG* 4.7 13.2 - - + +
527E THR* 3.9 9.4 - - - -
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Residues in contact with CYS 521 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299E THR* 3.6 24.9 - - - -
303E ARG* 4.2 4.3 - - - -
497E ASP 3.4 5.2 - - - -
498E THR* 3.8 13.9 - - + +
518E ILE* 4.2 11.4 - - + -
520E LYS* 1.3 82.1 - - - +
522E ARG* 1.3 58.9 + - - +
523E PHE* 4.4 0.9 - - - -
524E THR* 3.0 33.3 + - - +
525E GLY* 2.3 44.3 + - - +
526E ASP 4.2 4.5 - - - +
527E THR* 4.2 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