Contacts of the helix formed by residues 522 - 528 (chain C) in PDB entry 6NID
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 GLY 522 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521B GLY* 5.5 1.1 - - - -
499C GLU* 5.4 3.1 - - - -
502C GLY* 4.8 7.9 - - - -
519C MET* 3.0 22.0 + - - +
520C HIS 3.2 1.8 + - - -
521C GLY* 1.3 78.4 - - - +
523C MET* 1.3 66.8 + - - -
524C ILE 3.4 2.7 - - - -
525C HIS* 3.3 4.7 + - - +
526C ARG* 3.1 26.0 + - - +
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Residues in contact with MET 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B HIS* 5.2 13.7 - - + +
521B GLY* 6.5 0.7 - - - -
493C PHE* 3.8 30.7 - - + -
494C GLN 4.9 7.6 - - - +
497C THR* 5.4 2.5 - - - +
499C GLU* 3.5 45.1 - - - +
500C PRO 4.0 11.9 + - - +
501C MET 3.5 11.1 + - - +
522C GLY* 1.3 73.4 - - - -
524C ILE* 1.3 57.8 + - - +
526C ARG* 3.4 7.5 + - - +
527C GLN* 2.9 29.3 + - - +
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Residues in contact with ILE 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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491C VAL* 5.8 0.7 - - + -
493C PHE* 3.6 29.2 - - + -
501C MET* 3.0 34.6 + - + +
502C GLY* 4.5 1.8 - - - +
503C ILE* 3.5 31.2 - - + -
518C ILE* 4.2 10.3 - - + +
522C GLY 3.4 0.2 - - - -
523C MET* 1.3 72.2 - - - +
525C HIS* 1.3 67.2 + - - +
527C GLN* 3.3 15.6 + - - +
528C GLY* 3.0 20.3 + - - -
529C THR 4.4 1.9 + - - -
530C LEU* 3.9 37.6 + - + +
565C PHE* 4.7 9.0 - - + -
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Residues in contact with HIS 525 (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 GLY 5.2 0.2 + - - -
518C ILE* 3.6 21.7 - - + +
519C MET 3.4 20.6 - - - +
520C HIS* 3.4 49.9 + + - -
521C GLY 3.9 3.8 + - - +
522C GLY 3.3 5.9 + - - +
523C MET 3.3 0.4 - - - -
524C ILE* 1.3 79.3 - - - +
526C ARG* 1.3 82.8 + - - +
528C GLY* 3.1 15.7 + - - -
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Residues in contact with ARG 526 (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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521B GLY* 3.0 38.9 + - - +
522B GLY* 4.0 5.2 + - - -
523B MET* 4.1 19.0 - - - +
526B ARG* 3.6 34.4 - - - +
520C HIS* 4.3 9.9 - - - -
521C GLY* 4.0 9.9 - - - +
522C GLY 3.1 20.8 + - - +
523C MET* 3.8 6.7 - - - +
524C ILE 3.3 0.2 - - - -
525C HIS* 1.3 100.9 + - - +
527C GLN* 1.3 63.8 + - - +
528C GLY* 3.4 0.7 + - - -
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Residues in contact with GLN 527 (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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491C VAL* 4.0 12.6 - - - +
492C GLN 2.7 29.1 + - - -
493C PHE* 3.9 14.7 - - + +
523C MET 2.9 17.8 + - - +
524C ILE* 3.6 25.6 - - - +
525C HIS 3.3 0.2 - - - -
526C ARG* 1.3 75.9 - - - +
528C GLY* 1.3 60.9 + - - +
529C THR* 3.5 24.4 + - - +
530C LEU 4.9 1.0 + - - -
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Residues in contact with GLY 528 (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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524C ILE 3.0 10.5 + - - -
525C HIS* 3.1 13.5 + - - -
526C ARG 4.2 1.1 - - - -
527C GLN* 1.3 76.8 - - - +
529C THR* 1.3 59.8 + - - +
530C LEU 3.9 5.6 - - - -
531C HIS* 4.3 12.6 + - - -
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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