Contacts of the helix formed by residues 513 - 524 (chain A) in PDB entry 1XMI
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 ASP 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511A SER 4.6 2.0 - - - +
512A TYR* 1.3 79.3 - - - +
514A GLU* 1.3 66.4 + - - +
515A TYR* 3.7 8.5 + - - +
516A ARG* 3.1 37.0 + - + +
517A TYR* 3.0 26.5 + - - +
563A TYR* 2.9 12.4 + - - +
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Residues in contact with GLU 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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512A TYR* 2.7 35.0 + - + -
513A ASP* 1.3 74.8 + - - +
515A TYR* 1.3 64.6 + - - +
517A TYR* 3.8 1.6 - - - +
518A ARG* 2.9 65.4 + - + +
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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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513A ASP* 3.7 8.3 + - - +
514A GLU* 1.3 78.8 - - - +
516A ARG* 1.3 64.7 + - - +
518A ARG* 3.5 5.8 + - + +
519A SER* 2.9 47.2 + - - -
588C GLU* 2.9 45.3 + - + +
608C GLU* 5.7 11.0 - - + -
612C LYS* 4.3 22.4 - - + -
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Residues in contact with ARG 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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513A ASP* 3.1 27.1 + - + +
515A TYR* 1.3 80.3 - - + +
517A TYR* 1.3 62.3 + - - +
519A SER* 3.2 8.1 + - - -
520A VAL* 3.0 32.2 + - + +
562A VAL 3.2 17.3 + - - -
563A TYR* 2.5 48.4 + - + -
564A LYS 3.3 14.3 + - - -
565A ASP* 3.6 21.2 + - - +
569A TYR* 4.0 4.2 + - - -
598A LYS* 5.7 1.8 - - - +
593C LYS* 5.9 3.2 - - - +
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Residues in contact with TYR 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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502A ILE* 4.9 0.7 - - - +
503A LYS* 3.5 34.0 + - + -
506A ILE* 3.9 36.3 - - + +
507A ILE* 3.5 19.7 - - + -
512A TYR* 3.6 24.5 - + + -
513A ASP 3.0 18.2 + - - +
514A GLU 3.8 2.0 - - - +
516A ARG* 1.3 77.0 - - - +
518A ARG* 1.3 79.6 + - - +
520A VAL* 3.4 1.7 + - - +
521A ILE* 3.1 45.6 + - + +
530A ILE* 5.4 2.3 - - + +
537A ASP* 3.1 31.8 + - - +
563A TYR* 3.6 12.2 - + + -
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Residues in contact with ARG 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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503A LYS* 5.3 3.0 - - - +
512A TYR* 3.8 10.9 + - - -
514A GLU* 2.9 48.1 + - + +
515A TYR* 3.9 7.0 - - + +
517A TYR* 1.3 91.8 - - - +
519A SER* 1.3 66.6 + - - +
521A ILE* 3.4 30.4 - - - +
522A LYS* 3.0 33.8 + - - +
527A GLU* 4.8 1.4 - - - +
530A ILE* 5.7 2.4 - - - +
537A ASP* 4.3 10.3 + - - -
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Residues in contact with SER 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 TYR* 2.9 41.5 + - - -
516A ARG* 3.4 11.7 - - - -
518A ARG* 1.3 75.1 - - - +
520A VAL* 1.3 57.8 + - - +
522A LYS* 3.7 8.0 - - - +
523A ALA* 2.9 30.4 + - - +
594A LEU* 3.9 23.6 - - - +
588C GLU* 6.0 0.2 - - - +
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Residues in contact with VAL 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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506A ILE* 4.5 6.1 - - + -
516A ARG* 3.0 25.6 + - + +
517A TYR 3.7 5.2 - - - +
519A SER* 1.3 76.6 - - - +
521A ILE* 1.3 60.4 + - - +
523A ALA 3.4 0.5 + - - -
524A CYS* 2.9 33.1 + - - +
559A ALA* 3.4 41.1 - - + +
562A VAL* 4.4 5.6 - - + +
563A TYR* 4.0 31.0 - - + +
594A LEU* 4.0 20.4 - - + -
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Residues in contact with ILE 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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506A ILE* 3.9 28.0 - - + -
517A TYR* 3.1 35.0 + - + +
518A ARG* 3.4 43.7 - - - +
520A VAL* 1.3 79.4 - - + +
522A LYS* 1.3 55.2 + - - +
525A GLN 3.1 4.9 + - - -
526A LEU* 2.7 48.9 + - + -
527A GLU* 3.6 32.4 + - + +
530A ILE* 4.6 11.9 - - + -
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Residues in contact with LYS 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 ARG* 3.0 27.6 + - - +
519A SER* 3.7 7.9 - - - +
521A ILE* 1.3 76.0 - - - +
523A ALA* 1.3 64.8 + - - +
525A GLN* 3.2 17.4 + - - +
527A GLU* 2.8 41.8 + - - +
589A SER* 5.4 0.5 - - - -
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Residues in contact with ALA 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 SER 2.9 19.0 + - - +
520A VAL 3.4 2.7 + - - +
522A LYS* 1.3 76.6 - - - +
524A CYS* 1.3 60.3 + - - +
525A GLN* 3.5 2.4 + - - +
586A ILE* 4.0 11.8 - - - +
589A SER* 2.7 47.3 + - - +
590A CYS* 4.2 5.7 - - + +
594A LEU* 3.8 25.1 - - + -
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Residues in contact with CYS 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 VAL* 2.9 22.6 + - - +
523A ALA* 1.3 74.5 - - - +
525A GLN* 1.3 69.2 + - - +
526A LEU* 3.4 10.1 + - + +
555A ARG* 3.2 38.0 + - + +
558A LEU* 4.0 11.2 - - + -
559A ALA* 3.8 27.8 - - + -
562A VAL* 5.1 0.4 - - - -
586A ILE* 4.1 9.0 - - + -
590A CYS* 3.9 26.7 - - - -
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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