Contacts of the helix formed by residues 514 - 530 (chain A) in PDB entry 1WSU
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 THR 514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A SER* 3.5 13.5 + - - +
513A GLU* 1.3 80.5 - - + +
515A GLN* 1.3 67.3 + - - +
516A LYS 3.2 0.7 - - - -
517A LYS* 3.4 11.7 + - - +
518A LEU* 3.2 18.4 + - - +
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Residues in contact with GLN 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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511A GLY* 4.0 19.6 + - - -
512A SER* 3.8 21.1 - - - +
513A GLU 3.9 0.4 - - - +
514A THR* 1.3 84.6 + - - +
516A LYS* 1.3 62.2 + - + +
518A LEU* 3.1 33.5 + - - +
519A LEU* 3.2 16.5 + - + +
553A LEU* 4.0 25.3 - - + +
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Residues in contact with LYS 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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512A SER 4.0 18.7 + - - +
513A GLU* 2.9 40.1 + - - +
514A THR 3.2 0.6 - - - -
515A GLN* 1.3 79.9 - - + +
517A LYS* 1.3 60.8 + - - +
519A LEU* 3.4 24.7 + - + +
520A LYS* 3.4 15.9 + - - +
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Residues in contact with LYS 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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513A GLU 3.5 9.8 + - - +
514A THR* 3.4 13.8 + - - +
515A GLN 3.2 0.6 - - - -
516A LYS* 1.3 76.5 - - - +
518A LEU* 1.3 61.1 + - - +
519A LEU 3.2 0.2 - - - -
520A LYS* 3.3 8.5 + - + +
521A ASP* 2.8 66.4 + - - +
586B ASN 5.2 6.3 + - - -
589B SER* 5.7 2.2 - - - +
590B THR* 4.0 28.0 - - + +
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Residues in contact with LEU 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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514A THR 3.2 12.0 + - - +
515A GLN* 3.1 38.9 + - - +
517A LYS* 1.3 79.3 - - - +
519A LEU* 1.3 54.2 + - - +
521A ASP* 3.3 4.3 + - + -
522A LEU* 2.9 41.1 + - + +
543A PHE* 3.5 35.7 - - + -
545A LEU* 4.6 12.1 - - + -
553A LEU* 4.1 17.7 - - + -
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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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515A GLN* 3.2 17.2 + - + +
516A LYS* 3.6 19.1 - - + +
517A LYS 3.2 0.4 - - - -
518A LEU* 1.3 75.9 - - - +
520A LYS* 1.3 60.4 + - + +
522A LEU* 3.5 6.7 + - + +
523A GLU* 3.0 30.0 + - - +
553A LEU* 3.7 29.2 - - + +
556A TYR* 3.6 41.3 - - + +
557A LEU* 4.0 23.7 - - + +
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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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516A LYS 3.4 11.5 + - - +
517A LYS* 3.3 14.6 + - + +
518A LEU 3.2 0.2 - - - -
519A LEU* 1.3 79.1 - - + +
521A ASP* 1.3 59.7 + - - +
523A GLU* 3.7 15.3 + - - +
524A ASP* 2.6 39.4 + - - +
586B ASN* 3.0 47.1 - - + +
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Residues in contact with ASP 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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517A LYS* 2.8 58.0 + - - +
518A LEU* 3.3 3.9 + - - +
520A LYS* 1.3 79.8 - - - +
522A LEU* 1.3 57.7 + - - +
524A ASP* 3.7 9.8 + - - +
525A LYS* 3.1 20.3 + - - +
543A PHE* 3.5 29.0 - - + -
586B ASN* 5.9 1.7 - - - +
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Residues in contact with LEU 522 (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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518A LEU* 2.9 31.9 + - + +
519A LEU* 3.7 6.3 - - + +
520A LYS 3.2 0.2 - - - -
521A ASP* 1.3 75.6 - - - +
523A GLU* 1.3 67.4 + - - +
525A LYS* 3.0 18.2 + - + +
526A TYR* 3.2 23.4 + - + -
539A VAL* 3.5 32.3 - - + -
543A PHE* 3.9 17.7 - - + -
545A LEU* 4.9 1.6 - - + -
550A LEU* 4.3 7.9 - - + -
553A LEU* 4.0 39.9 - - + -
554A LEU* 4.5 3.4 - - + -
557A LEU* 4.0 15.0 - - + -
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Residues in contact with GLU 523 (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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519A LEU 3.0 18.9 + - - +
520A LYS* 3.7 18.1 + - - +
522A LEU* 1.3 76.9 - - - +
524A ASP* 1.3 54.6 + - - +
526A TYR* 2.9 11.1 + - - +
527A ARG* 2.7 61.3 + - - +
557A LEU* 4.5 7.1 - - + +
562A VAL* 3.2 39.1 - - + +
563A LEU* 5.2 0.7 - - - -
573A HIS* 3.0 17.7 + - + -
586B ASN* 5.7 3.8 - - - +
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Residues in contact with ASP 524 (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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520A LYS 2.6 26.3 + - - +
521A ASP* 3.9 10.1 - - - +
523A GLU* 1.3 76.3 - - - +
525A LYS* 1.3 65.1 + - - +
527A ARG* 4.0 11.9 + - - -
528A VAL* 2.9 34.9 + - + +
582B GLU 4.5 0.7 - - - +
583B VAL* 3.9 30.1 + - + +
586B ASN* 2.9 32.2 - - - +
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Residues in contact with LYS 525 (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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521A ASP 3.1 11.2 + - - +
522A LEU* 3.0 13.6 + - - +
524A ASP* 1.3 76.3 - - - +
526A TYR* 1.3 63.9 + - + +
528A VAL* 4.2 2.0 - - - +
529A SER* 3.0 43.0 + - - +
534A PRO* 4.0 28.4 - - + +
538A GLU* 5.8 2.2 - - - +
539A VAL* 5.4 2.7 - - + -
542A SER* 3.8 26.4 + - - -
543A PHE* 3.7 23.8 - - + -
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Residues in contact with TYR 526 (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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522A LEU* 3.2 28.4 + - + -
523A GLU 2.9 7.4 + - - +
525A LYS* 1.3 82.3 - - + +
527A ARG* 1.3 59.9 + - - +
529A SER* 4.1 3.1 - - - -
530A ARG* 2.9 28.2 + - - +
533A PRO* 4.1 4.9 - - + +
534A PRO* 3.9 27.5 + - + -
535A SER 4.7 2.6 + - - -
536A PHE* 5.2 0.9 + - - -
539A VAL* 3.4 30.8 - - + +
554A LEU* 4.0 21.6 - - + +
563A LEU* 3.9 36.8 - - + -
569A GLU 5.7 0.3 + - - -
571A TYR* 3.2 50.4 - - + +
572A TRP* 4.6 1.3 - - - -
573A HIS* 4.0 12.9 + - + +
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Residues in contact with ARG 527 (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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523A GLU* 2.7 47.2 + - - +
524A ASP* 3.9 12.8 + - - +
526A TYR* 1.3 76.0 - - - +
528A VAL* 1.3 63.1 + - - +
530A ARG* 3.4 6.2 + - - +
573A HIS* 3.3 34.0 + - + +
575A GLN* 4.3 7.1 - - - +
576A ALA* 5.7 0.4 - - - +
530B ARG* 3.2 22.0 + - - -
531B TRP* 4.5 3.4 - - + -
579B GLU* 2.6 62.5 + - - +
582B GLU* 3.3 35.1 - - - +
583B VAL* 3.8 18.8 - - + -
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Residues in contact with VAL 528 (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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524A ASP* 2.9 23.6 + - + +
525A LYS* 4.2 2.0 - - - +
527A ARG* 1.3 75.9 - - - +
529A SER* 1.3 64.6 + - - +
530A ARG* 3.6 0.5 - - - +
530B ARG* 3.0 22.7 + - - +
531B TRP* 4.1 15.3 - - + -
583B VAL* 4.3 11.4 - - + -
601B ALA 3.4 25.4 - - - +
602B LEU 4.2 18.6 - - - +
603B GLY* 4.8 4.9 - - - +
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Residues in contact with SER 529 (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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525A LYS* 3.0 32.7 + - - +
526A TYR 4.1 1.3 - - - -
528A VAL* 1.3 78.1 - - - +
530A ARG* 1.3 64.9 + - - +
531A TRP 3.1 1.4 + - - -
532A GLN* 3.0 34.7 + - - +
533A PRO* 3.8 1.8 - - - -
534A PRO* 3.6 26.5 - - - +
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Residues in contact with ARG 530 (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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526A TYR 2.9 18.1 + - - +
527A ARG 3.7 2.0 - - - +
528A VAL 3.1 0.8 - - - +
529A SER* 1.3 75.9 - - - +
531A TRP* 1.3 110.1 + - + +
532A GLN* 3.3 1.3 - - - +
533A PRO* 3.5 15.2 - - - +
572A TRP* 4.3 5.2 - - - -
573A HIS 5.2 1.4 + - - -
576A ALA* 3.7 25.1 - - + +
579A GLU* 3.0 30.9 + - - +
527B ARG 3.1 28.5 + - - -
528B VAL 3.4 12.7 + - - -
530B ARG* 3.1 60.7 - - - +
579B GLU* 4.6 2.8 + - - +
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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