Contacts of the helix formed by residues 513 - 524 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A GLU* 5.3 4.9 - - - +
511C SER 4.8 1.1 - - - +
512C TYR* 1.3 78.8 - - - +
514C GLU* 1.3 66.2 + - - +
515C TYR* 3.4 12.0 + - - +
516C ARG* 3.2 31.7 + - + +
517C TYR* 2.9 25.1 + - - +
563C TYR* 2.8 15.0 + - - +
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Residues in contact with GLU 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512C TYR* 2.7 40.7 + - + -
513C ASP* 1.3 73.2 + - - +
515C TYR* 1.3 58.1 + - - +
517C TYR* 3.8 3.1 - - - +
518C ARG* 3.1 48.3 + - - +
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Residues in contact with TYR 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A GLU* 4.7 13.9 - - + +
450A ARG 3.3 16.3 + - - -
451A GLY* 3.0 30.4 + - - -
452A GLN* 3.3 35.4 - - + +
596A ALA 4.9 1.7 + - - -
597A ASN* 5.1 4.5 + - - -
614A ASP* 3.5 26.5 - - - -
513C ASP* 3.4 8.5 + - - +
514C GLU* 1.3 76.0 - - - +
516C ARG* 1.3 62.1 + - + +
518C ARG* 3.8 16.0 - - + +
519C SER* 2.8 57.4 + - - -
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Residues in contact with ARG 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513C ASP* 3.2 26.5 + - + +
515C TYR* 1.3 81.7 - - + +
517C TYR* 1.3 62.1 + - - +
519C SER* 3.4 5.9 + - - -
520C VAL* 3.1 33.5 + - + +
562C VAL 3.9 7.6 + - - -
563C TYR* 2.6 49.3 + - + +
564C LYS 3.4 14.6 + - - -
565C ASP* 3.5 26.2 + - - +
569C TYR* 3.9 5.5 + - - -
598C LYS* 5.0 6.5 - - - +
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Residues in contact with TYR 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502C ILE 4.6 0.2 - - - -
503C LYS* 3.6 33.8 + - + -
506C ILE* 4.0 37.1 - - + +
507C ILE* 3.6 19.3 - - + -
512C TYR* 3.6 28.7 - + + -
513C ASP 2.9 18.4 + - - +
514C GLU* 3.8 4.0 - - - +
516C ARG* 1.3 76.5 - - - +
518C ARG* 1.3 64.3 + - + +
520C VAL* 3.3 3.2 + - - +
521C ILE* 3.0 46.5 + - + +
530C ILE* 4.2 6.1 - - - +
537C ASP* 2.7 32.2 + - - +
563C TYR* 3.6 11.1 - + + -
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Residues in contact with ARG 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A GLN* 5.1 1.4 - - - +
611A LYS 5.9 0.8 + - - -
612A LYS 5.0 4.8 + - - -
613A ALA 4.5 5.9 + - - -
614A ASP* 3.1 45.0 + - - +
514C GLU* 3.1 34.9 + - - +
515C TYR* 3.8 21.4 - - + +
517C TYR* 1.3 76.6 - - + +
519C SER* 1.3 63.6 + - - +
521C ILE* 3.3 17.4 - - + +
522C LYS* 3.1 51.1 + - + +
527C GLU* 5.6 2.2 - - - +
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Residues in contact with SER 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A ASN* 4.8 5.2 + - - -
515C TYR* 2.8 53.3 + - - -
516C ARG* 3.6 7.2 - - - -
518C ARG* 1.3 76.9 - - - +
520C VAL* 1.3 57.9 - - - +
522C LYS* 3.7 9.2 - - - +
523C ALA* 3.1 28.9 + - - +
594C LEU* 4.0 20.4 - - - +
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Residues in contact with VAL 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C ILE* 4.5 9.4 - - + -
516C ARG* 3.1 24.7 + - + +
517C TYR 3.7 4.0 - - - +
519C SER* 1.3 74.2 - - - +
521C ILE* 1.3 60.6 + - + +
523C ALA 3.3 0.5 + - - -
524C CYS* 2.9 33.8 + - - +
559C ALA* 3.5 41.5 - - + +
562C VAL* 3.9 24.0 - - + +
563C TYR* 3.9 19.7 - - + -
594C LEU* 3.9 12.1 - - + -
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Residues in contact with ILE 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C ILE* 4.0 19.1 - - + -
517C TYR* 3.0 52.4 + - + +
518C ARG* 3.3 23.8 - - + +
520C VAL* 1.3 78.4 - - + +
522C LYS* 1.3 58.6 + - - +
524C CYS 4.6 0.2 - - - +
525C GLN 3.2 1.9 + - - -
526C LEU* 2.7 46.9 + - + +
527C GLU* 3.6 20.8 + - + +
530C ILE* 4.0 21.3 - - + -
537C ASP* 4.8 2.2 - - - +
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Residues in contact with LYS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A CYS* 5.7 6.3 - - - -
612A LYS* 3.2 34.9 + - - +
518C ARG* 3.1 44.2 + - + +
519C SER* 3.7 7.4 - - - +
521C ILE* 1.3 74.5 - - - +
523C ALA* 1.3 66.1 + - - +
525C GLN* 3.1 17.4 + - - +
527C GLU* 3.4 39.2 + - + +
589C SER* 4.9 1.4 + - - -
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Residues in contact with ALA 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A ASN* 5.4 1.6 - - - +
519C SER 3.1 16.4 + - - +
520C VAL 3.8 1.1 - - - +
522C LYS* 1.3 78.8 - - - +
524C CYS* 1.3 60.2 + - - +
525C GLN* 3.4 1.5 + - - +
586C ILE* 4.0 5.0 - - - +
589C SER* 2.7 50.0 + - - +
590C CYS* 3.8 11.5 - - + +
594C LEU* 3.7 25.8 - - + -
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Residues in contact with CYS 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520C VAL* 2.9 22.1 + - - +
523C ALA* 1.3 76.5 - - - +
525C GLN* 1.3 66.9 + - - +
526C LEU* 3.3 7.2 + - + -
555C ARG* 3.0 38.9 - - + +
558C LEU* 4.0 11.9 - - + -
559C ALA* 3.8 31.4 - - + -
562C VAL* 5.0 1.3 - - - -
586C ILE* 3.9 8.0 - - - +
590C CYS* 4.0 26.0 - - - -
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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