Contacts of the helix formed by residues 513 - 524 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511B SER* 4.6 3.6 - - - +
512B TYR* 1.3 79.3 - - - +
514B GLU* 1.3 64.8 + - - +
515B TYR 3.4 4.9 + - - -
516B ARG* 2.9 41.4 + - + +
517B TYR* 3.0 24.1 + - - +
563B TYR* 2.7 14.9 + - + +
528D GLU* 5.3 2.6 - - - +
672D GLU* 3.2 33.6 - - - +
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Residues in contact with GLU 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A GLY 5.0 1.6 - - - +
488A ILE* 5.0 6.2 + - - +
564A LYS* 5.9 2.7 - - - +
512B TYR* 2.5 41.4 + - + -
513B ASP* 1.3 74.6 + - - +
515B TYR* 1.3 63.7 + - - +
517B TYR* 3.3 2.1 + - - +
518B ARG* 3.0 54.7 + - + +
668D ARG* 3.7 33.7 + - + +
669D PHE* 3.8 32.8 - - + -
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Residues in contact with TYR 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A ARG* 2.9 55.0 + - - +
510A VAL* 5.9 10.5 - - + +
564A LYS* 5.0 16.2 - - + -
513B ASP* 3.4 5.9 + - - +
514B GLU* 1.3 79.7 - - - +
516B ARG* 1.3 66.0 + - - +
518B ARG* 3.4 1.0 + - - -
519B SER* 3.0 28.0 + - - -
668D ARG 5.1 1.7 + - - +
671D LEU 4.9 2.7 + - - +
672D GLU* 3.6 39.3 - - + -
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Residues in contact with ARG 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B ASP* 2.9 27.1 + - - +
515B TYR* 1.3 75.7 - - - +
517B TYR* 1.3 67.2 + - - +
519B SER* 3.2 8.7 + - - -
520B VAL* 3.0 32.6 + - + +
562B VAL 3.3 16.3 + - - -
563B TYR* 2.6 46.9 + - + +
564B LYS 3.4 10.9 + - - -
565B ASP* 3.6 26.0 + - - +
569B TYR* 3.5 9.5 + - - -
598B LYS* 5.6 3.0 - - - +
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Residues in contact with TYR 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B LYS* 3.5 44.6 + - + +
506B ILE* 3.8 35.0 - - + +
507B ILE* 3.7 23.3 - - + -
512B TYR* 3.4 23.1 - + + -
513B ASP 3.0 19.7 + - - +
514B GLU 3.4 4.3 - - - +
516B ARG* 1.3 77.0 - - - +
518B ARG* 1.3 88.7 + - - +
520B VAL* 3.3 2.4 + - - +
521B ILE* 3.0 41.9 + - + +
530B ILE* 4.2 13.8 - - + +
563B TYR* 3.6 10.0 - + + -
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Residues in contact with ARG 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A HIS* 5.8 2.9 + - - -
485A SER* 5.4 2.4 - - - +
486A GLY* 3.3 35.9 + - - +
487A ARG* 3.6 36.8 - - + +
503B LYS* 4.3 9.1 - - - +
512B TYR* 3.8 15.0 + - - -
514B GLU* 3.0 38.8 + - + +
515B TYR* 5.0 0.2 - - - -
517B TYR* 1.3 99.0 - - - +
519B SER* 1.3 57.0 + - - +
521B ILE* 3.4 13.2 + - - +
522B LYS* 3.0 34.2 + - - +
527B GLU* 4.6 1.6 - - - +
530B ILE* 4.9 13.3 - - - +
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Residues in contact with SER 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A ARG* 2.6 28.4 + - - +
515B TYR* 3.0 24.6 + - - -
516B ARG* 3.4 11.2 - - - -
518B ARG* 1.3 76.3 - - - +
520B VAL* 1.3 57.7 + - - +
522B LYS* 3.4 5.8 + - - +
523B ALA* 2.9 29.6 + - - +
594B LEU* 3.9 23.2 - - - +
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Residues in contact with VAL 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B ILE* 4.9 4.0 - - + -
516B ARG* 3.0 25.6 + - + +
517B TYR 3.8 4.3 - - - +
519B SER* 1.3 74.1 - - - +
521B ILE* 1.3 61.3 + - + +
524B CYS* 3.0 35.2 + - - +
559B ALA* 3.5 41.3 - - + +
562B VAL* 4.3 5.6 - - + +
563B TYR* 4.0 31.4 - - + +
594B LEU* 4.0 21.5 - - + -
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Residues in contact with ILE 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B ILE* 3.6 21.5 - - + -
517B TYR* 3.0 41.6 + - + +
518B ARG* 3.6 14.4 - - - +
519B SER 3.4 0.2 - - - -
520B VAL* 1.3 79.8 - - + +
522B LYS* 1.3 60.4 + - - +
524B CYS* 3.9 0.6 - - - -
525B GLN 3.2 2.6 + - - -
526B LEU* 2.9 39.2 + - + -
527B GLU* 3.5 37.8 + - + +
530B ILE* 3.3 33.2 - - + -
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Residues in contact with LYS 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A SER* 3.8 7.9 + - - +
486A GLY* 4.0 1.1 - - - -
487A ARG* 3.9 36.1 - - - +
567A ASP* 2.9 30.3 + - - -
518B ARG 3.0 15.8 + - - +
519B SER* 3.5 8.3 - - - +
520B VAL 3.3 0.2 - - - -
521B ILE* 1.3 76.6 - - - +
523B ALA* 1.3 63.9 + - - +
525B GLN* 3.2 17.3 + - - +
527B GLU* 2.7 44.6 + - - +
589B SER* 5.0 1.4 + - - -
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Residues in contact with ALA 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B SER 2.9 16.6 + - - +
520B VAL 3.4 2.2 + - - +
522B LYS* 1.3 76.4 - - - +
524B CYS* 1.3 59.7 + - - +
525B GLN* 3.3 2.0 + - - +
586B ILE* 4.0 6.6 - - - +
589B SER* 2.6 50.4 + - - +
590B CYS* 3.9 12.0 - - + +
594B LEU* 3.9 22.4 - - + -
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Residues in contact with CYS 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B VAL* 3.0 23.6 + - - +
521B ILE 4.5 0.2 - - - +
523B ALA* 1.3 74.9 - - - +
525B GLN* 1.3 66.0 + - - +
526B LEU* 3.3 12.1 + - + -
555B ARG* 3.0 40.8 - - + +
558B LEU* 4.3 9.4 - - + -
559B ALA* 3.8 27.4 - - - -
562B VAL* 4.9 0.7 - - - -
586B ILE* 4.3 8.7 - - + -
590B CYS* 3.9 25.6 - - - -
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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