Contacts of the helix formed by residues 511 - 522 (chain A) in PDB entry 3GVU
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 PRO 511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383A ALA* 6.3 0.2 - - + -
509A GLY 3.3 9.2 - - - +
510A CYS* 1.3 82.6 - - - +
512A PRO* 1.4 69.1 - - + +
513A LYS* 3.1 5.8 - - + +
514A VAL* 2.9 35.2 + - + +
515A TYR* 3.1 9.9 + - - +
1002A STI 3.7 51.1 - - + +
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Residues in contact with PRO 512 (chain A).
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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506A GLN* 3.8 17.3 - - - +
510A CYS 3.4 3.3 - - - +
511A PRO* 1.4 85.1 - - + +
513A LYS* 1.3 65.8 + - + +
515A TYR* 3.4 3.3 + - + +
516A GLU* 2.9 30.0 + - - +
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Residues in contact with LYS 513 (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 PRO* 3.1 4.4 - - + -
512A PRO* 1.3 82.4 - - + +
514A VAL* 1.3 64.3 + - + +
516A GLU* 2.7 32.9 + - - +
517A LEU* 3.2 17.3 + - - +
542A MET* 3.6 34.3 - - + +
1002A STI 6.1 0.9 - - + -
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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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475A LEU* 3.9 25.6 - - + +
510A CYS* 3.7 15.7 - - - -
511A PRO* 2.9 18.9 + - + +
513A LYS* 1.3 76.5 - - + +
515A TYR* 1.3 63.5 + - - +
517A LEU* 3.1 6.7 + - - +
518A MET* 3.0 22.1 + - + +
539A PHE* 5.2 1.8 - - + -
542A MET* 4.2 13.5 - - - -
1002A STI 3.5 60.3 - - + +
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Residues in contact with TYR 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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503A ARG 4.6 0.3 + - - -
504A MET 2.7 25.9 + - - -
505A GLU* 3.7 5.9 + - - -
506A GLN* 3.4 62.7 + - + -
507A PRO* 4.3 1.1 - - + -
510A CYS* 3.7 5.5 - - - -
511A PRO 3.1 9.1 + - - +
512A PRO* 3.8 6.5 - - + +
514A VAL* 1.3 74.7 - - - +
516A GLU* 1.3 65.6 + - - +
518A MET* 3.2 24.5 + - - +
519A ARG* 2.8 68.7 + - + +
522A TRP* 4.6 1.1 - + - -
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Residues in contact with GLU 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 PRO 2.9 18.5 + - - +
513A LYS* 2.7 42.4 + - - +
514A VAL 3.3 0.2 - - - -
515A TYR* 1.3 76.4 - - - +
517A LEU* 1.3 57.5 + - - +
519A ARG* 3.4 7.6 + - - +
520A ALA* 3.0 27.4 + - + +
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Residues in contact with LEU 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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475A LEU* 4.3 6.5 - - + -
513A LYS 3.2 9.2 + - - +
514A VAL* 3.1 9.3 + - - +
516A GLU* 1.3 79.2 - - - +
518A MET* 1.3 65.5 + - - +
520A ALA* 3.2 6.4 + - + +
521A CYS* 3.0 27.3 + - - -
530A PRO* 4.5 12.3 - - + -
534A GLU 5.6 0.4 - - - +
535A THR* 4.1 26.2 - - + +
538A ALA* 4.2 19.1 - - + -
539A PHE* 3.5 43.1 - - + -
542A MET* 4.2 12.6 - - + -
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Residues in contact with MET 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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472A GLY* 3.7 17.7 - - - +
475A LEU* 3.9 25.3 - - + +
476A TRP* 3.6 46.4 - - + +
479A ALA* 3.9 15.3 - - + -
507A PRO* 4.2 4.7 - - + -
510A CYS* 4.0 17.9 - - - -
514A VAL* 3.0 10.0 + - + +
515A TYR* 3.2 24.7 - - + +
517A LEU* 1.3 76.4 - - - +
519A ARG* 1.3 62.1 + - - +
521A CYS* 3.1 19.2 + - - +
522A TRP* 3.2 32.7 + - + -
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Residues in contact with ARG 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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501A GLY 5.0 4.9 + - - -
503A ARG* 3.7 28.5 + - - +
504A MET 4.6 0.2 + - - -
505A GLU* 6.0 0.2 + - - -
515A TYR* 2.8 73.3 + - + +
516A GLU* 3.7 7.0 - - - +
517A LEU 3.3 0.2 - - - -
518A MET* 1.3 80.4 - - - +
520A ALA* 1.3 60.8 + - - +
522A TRP* 3.2 32.6 + - - +
523A LYS* 3.4 13.0 + - - +
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Residues in contact with ALA 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 GLU* 3.0 14.9 + - + +
517A LEU* 3.2 13.4 + - + +
519A ARG* 1.3 75.0 - - - +
521A CYS* 1.3 63.4 + - - +
522A TRP 3.3 0.5 + - - -
523A LYS* 3.3 37.5 + - - +
528A ASP 5.6 0.2 - - - +
529A ARG* 3.6 4.0 - - - -
530A PRO* 3.4 29.1 - - + +
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Residues in contact with CYS 521 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A VAL* 3.4 40.6 - - - +
469A TRP* 3.4 12.0 + - - -
471A PHE* 4.2 13.7 - - - -
472A GLY* 3.8 19.7 - - - -
475A LEU* 5.7 0.4 - - - -
517A LEU* 3.0 27.7 + - - -
518A MET* 3.1 9.6 + - - +
520A ALA* 1.3 76.3 - - - +
522A TRP* 1.3 57.3 + - + +
523A LYS 3.4 0.7 - - - -
529A ARG* 3.3 22.7 + - - -
530A PRO* 4.2 9.0 - - - -
535A THR* 4.6 2.5 - - - -
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Residues in contact with TRP 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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469A TRP* 3.2 41.0 + + + -
472A GLY* 3.4 23.8 - - - -
473A VAL* 3.3 25.4 - - + +
476A TRP* 4.1 2.5 - + + -
486A TYR* 5.3 4.5 - - - -
503A ARG* 2.8 51.6 + - + +
504A MET* 3.7 57.9 - - + -
515A TYR* 4.6 0.2 - + - -
518A MET* 3.4 36.6 - - + -
519A ARG* 3.2 31.4 + - - +
520A ALA 3.1 1.0 - - - -
521A CYS* 1.3 81.3 - - - +
523A LYS* 1.3 64.8 + - - +
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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