Contacts of the helix formed by residues 517 - 526 (chain A) in PDB entry 5M64
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 ALA 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515A ASN* 3.2 0.6 - - - +
516A ILE* 1.3 92.3 - - + +
518A GLU* 1.3 62.7 + - - +
520A ARG* 3.3 20.7 - - - +
521A GLN* 3.7 8.7 + - - +
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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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515A ASN* 3.7 15.0 + - + +
517A ALA* 1.3 78.6 - - - +
519A LEU* 1.3 64.2 + - - +
521A GLN* 3.2 13.4 + - - +
522A ALA* 3.1 21.1 + - - +
531A PRO* 4.8 13.3 - - - +
579A ARG* 3.3 33.9 + - - +
582A LYS* 5.2 1.9 - - - +
584A ARG* 4.6 14.4 - - - +
115F THR* 5.6 6.7 - - + +
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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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509A GLU* 3.8 23.1 - - - +
511A VAL* 3.7 35.7 - - + -
512A THR 5.5 0.9 - - - +
515A ASN* 3.0 25.9 + - + +
516A ILE* 5.2 0.2 - - - -
518A GLU* 1.3 75.6 - - - +
520A ARG* 1.3 60.3 + - - +
522A ALA* 3.2 8.6 + - + +
523A VAL* 3.0 37.5 + - + +
561A LEU* 4.5 12.1 - - + -
577A VAL* 3.6 36.3 - - + +
579A ARG* 4.4 19.5 - - - +
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Residues in contact with ARG 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 ILE 3.3 21.7 + - - +
517A ALA* 3.3 18.4 - - - +
519A LEU* 1.3 78.7 - - - +
521A GLN* 1.3 60.3 + - + +
523A VAL* 4.2 1.4 - - - +
524A ILE* 3.0 34.4 + - - +
558A ALA* 4.8 13.7 + - + +
559A ASN* 4.6 16.0 - - - +
561A LEU* 3.7 24.5 - - + +
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Residues in contact with GLN 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 ALA 3.7 9.8 + - - +
518A GLU* 3.2 18.5 + - - +
519A LEU 3.1 0.6 - - - -
520A ARG* 1.3 81.4 - - + +
522A ALA* 1.3 64.7 + - - +
524A ILE* 3.3 17.1 - - - +
525A ASN* 2.8 61.6 + - - +
531A PRO* 5.2 9.0 - - + -
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Residues in contact with ALA 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* 3.1 13.3 + - - +
519A LEU* 3.2 13.6 + - + +
521A GLN* 1.3 76.5 - - - +
523A VAL* 1.3 61.5 + - - +
526A GLY 3.5 3.8 + - - -
531A PRO* 3.8 13.5 - - + +
532A GLY* 3.2 19.4 - - - +
533A ALA* 2.9 30.3 + - + -
579A ARG* 4.2 25.4 - - + +
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Residues in contact with VAL 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 19.1 + - + +
520A ARG* 4.2 4.7 - - - +
522A ALA* 1.3 78.1 - - - +
524A ILE* 1.3 64.8 + - - +
525A ASN 3.2 2.7 + - - -
526A GLY* 3.6 10.0 + - - -
533A ALA* 4.4 3.8 - - + -
536A ILE* 4.2 16.4 - - + -
546A LEU* 4.9 8.0 - - + +
554A ARG* 4.0 18.4 - - - +
557A LEU* 4.7 14.8 - - + +
558A ALA* 4.3 23.1 - - + +
561A LEU* 4.8 9.9 - - + -
577A VAL* 4.0 31.0 - - + -
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Residues in contact with ILE 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 ARG* 3.0 23.9 + - - +
521A GLN* 3.3 30.5 - - - +
523A VAL* 1.3 76.5 - - - +
525A ASN* 1.3 65.5 + - - +
551A VAL* 4.5 12.5 - - + +
554A ARG* 4.2 23.1 - - + +
555A LYS* 4.9 21.8 - - + -
558A ALA* 4.8 8.7 - - + +
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Residues in contact with ASN 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 GLN* 2.8 47.0 + - - +
524A ILE* 1.3 82.5 + - - +
526A GLY* 1.3 56.3 + - - +
528A ASP 4.6 0.5 + - - -
529A LYS* 3.3 50.7 + - + +
531A PRO* 2.9 29.8 - - - +
532A GLY* 4.1 0.4 - - - -
554A ARG* 2.4 29.1 + - - -
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Residues in contact with GLY 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 ALA 3.5 7.9 + - - -
523A VAL 3.6 7.0 + - - -
525A ASN* 1.3 76.5 - - - +
527A PRO* 1.3 70.5 - - - +
528A ASP 3.1 6.4 + - - -
529A LYS 3.0 21.3 - - - +
532A GLY* 3.3 7.6 - - - -
533A ALA 3.6 13.5 - - - -
546A LEU* 5.4 1.8 - - - -
554A ARG* 3.6 10.5 - - - -
580A HIS* 3.6 0.5 - - - -
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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