Contacts of the helix formed by residues 513 - 524 (chain A) in PDB entry 3RC3
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 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A TRP* 4.5 17.8 - - + -
511A HIS* 4.4 13.5 - - + +
512A PRO* 1.3 76.1 - - - +
514A ALA* 1.3 64.5 + - - +
515A GLU* 3.6 17.6 + - - +
516A GLN* 2.8 41.8 + - - +
517A ILE* 3.1 21.3 + - - +
572A TYR* 3.8 3.8 - - - -
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Residues in contact with ALA 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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513A THR* 1.3 72.3 - - - +
515A GLU* 1.3 62.8 + - - +
517A ILE* 3.4 2.4 + - - +
518A GLU* 2.9 29.5 + - - +
568A LEU* 4.3 1.6 - - - +
569A ARG* 3.6 29.8 - - - +
572A TYR* 3.6 40.3 + - + -
573A VAL* 6.4 0.9 - - + -
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Residues in contact with GLU 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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513A THR* 3.6 19.4 - - - +
514A ALA* 1.3 74.1 + - - +
516A GLN* 1.3 68.2 + - + +
518A GLU* 3.3 9.6 + - - +
519A MSE 3.0 26.7 + - - +
569A ARG* 3.1 35.2 + - - +
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Residues in contact with GLN 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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182A ILE* 3.5 34.4 + - + +
184A ASP 4.7 0.4 + - - -
185A LEU* 3.1 23.7 - - - +
191A TRP* 3.0 34.9 - - + -
511A HIS 4.3 0.5 - - - +
512A PRO* 3.3 10.6 - - + +
513A THR* 2.8 42.1 + - - +
515A GLU* 1.3 75.9 - - + +
517A ILE* 1.3 60.1 + - - +
519A MSE 3.2 4.5 + - - +
520A PHE* 3.0 25.5 + - - +
536A PHE* 3.6 19.3 - - + -
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Residues in contact with ILE 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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512A PRO* 3.8 12.8 - - + -
513A THR 3.1 19.8 + - - +
514A ALA 4.0 2.9 - - - +
516A GLN* 1.3 72.3 - - - +
518A GLU* 1.3 66.0 + - - +
520A PHE* 3.1 6.8 + - + +
521A ALA* 2.9 21.0 + - - +
529A LEU* 3.7 29.8 - - + -
532A LEU* 4.3 12.3 - - + +
533A ILE* 3.7 26.2 - - + -
536A PHE* 3.7 36.8 - - + -
568A LEU* 4.2 11.9 - - + -
572A TYR* 4.0 15.0 - - + -
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Residues in contact with GLU 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 ALA 2.9 17.0 + - - +
515A GLU* 3.7 7.4 - - - +
516A GLN 3.2 0.2 - - - -
517A ILE* 1.3 76.7 - - - +
519A MSE 1.3 68.0 + - + +
521A ALA* 3.1 5.5 + - - +
522A TYR* 3.0 53.1 + - + -
568A LEU* 3.2 25.7 - - + +
569A ARG* 2.6 45.9 + - - +
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Residues in contact with MSE 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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182A ILE* 3.7 32.8 - - + -
515A GLU 3.0 18.2 + - - +
516A GLN* 3.6 5.4 - - - +
518A GLU* 1.3 80.3 - - + +
520A PHE* 1.3 61.0 + - - +
522A TYR* 3.2 35.8 + - + +
523A HIS* 2.7 36.9 + - + -
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Residues in contact with PHE 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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179A LEU* 3.5 55.2 - - + -
182A ILE* 3.8 21.1 - - + -
183A SER* 4.1 4.3 - - - -
516A GLN 3.0 12.1 + - - +
517A ILE* 3.1 13.0 + - + +
519A MSE 1.3 77.4 - - - +
521A ALA* 1.3 56.8 + - - +
523A HIS* 3.1 7.5 + - - +
524A LEU* 3.0 31.2 + - + +
532A LEU* 4.0 33.9 - - + -
535A ILE* 3.8 17.9 - - + -
536A PHE* 3.5 46.7 - + + -
539A PHE* 4.4 3.4 - - + -
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Residues in contact with ALA 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 ILE 2.9 7.3 + - - +
518A GLU 3.1 8.3 + - - +
520A PHE* 1.3 74.8 - - - +
522A TYR* 1.4 67.2 + - + +
524A LEU 4.2 4.0 - - - +
525A PRO* 3.1 28.7 - - + +
532A LEU* 3.7 14.3 - - + +
568A LEU* 3.4 37.5 - - + -
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Residues in contact with TYR 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 GLU* 3.0 49.3 + - + -
519A MSE 3.2 32.7 + - + +
521A ALA* 1.4 78.2 - - + +
523A HIS* 1.3 66.9 + - + +
525A PRO* 3.9 11.0 - - - +
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Residues in contact with HIS 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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171A PRO* 4.7 5.4 - - - +
175A CYS* 4.0 22.1 - - + -
178A ASP* 3.8 31.7 + - + +
179A LEU* 3.8 19.1 - - + -
182A ILE* 3.4 22.6 - - + +
519A MSE 2.7 35.6 + - + -
520A PHE 3.1 8.5 + - - +
522A TYR* 1.3 81.0 - - + +
524A LEU* 1.3 68.6 + - + +
525A PRO* 3.4 7.3 - - - +
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Residues in contact with LEU 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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171A PRO* 4.0 15.9 - - + -
172A VAL* 3.7 50.7 - - + +
175A CYS* 4.2 6.1 - - - -
179A LEU* 4.2 12.6 - - + -
520A PHE* 3.0 16.9 + - + +
521A ALA* 3.4 6.6 - - - +
523A HIS* 1.3 88.7 - - + +
525A PRO* 1.3 59.0 - - - +
526A ASP 3.1 10.5 + - - -
527A ALA* 3.2 20.8 + - + +
532A LEU* 3.8 24.3 - - + +
535A ILE* 4.3 17.0 - - + -
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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