Contacts of the helix formed by residues 522 - 528 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B PRO 5.9 0.4 - - - -
501B MET 4.5 4.3 - - - -
502B GLY* 4.5 10.1 - - - -
519B MET* 3.1 18.0 + - - +
520B HIS 3.3 0.9 - - - +
521B GLY* 1.3 80.2 - - - +
523B MET* 1.3 62.4 + - - -
524B ILE 3.3 2.7 - - - -
525B HIS* 3.3 4.4 + - - +
526B ARG* 3.0 27.0 + - - +
521C GLY* 5.3 2.2 - - - -
526C ARG* 4.0 4.4 + - - -
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Residues in contact with MET 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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493B PHE* 3.7 32.7 - - + -
494B GLN 5.9 1.1 - - - +
497B THR* 5.4 0.9 - - - +
499B GLU* 3.5 27.8 - - + +
500B PRO 3.1 24.9 - - - +
501B MET* 3.4 8.8 + - - +
522B GLY* 1.3 69.2 - - - -
524B ILE* 1.3 61.8 + - - +
526B ARG* 3.4 2.6 + - - +
527B GLN* 3.0 28.2 + - - +
520C HIS* 4.1 21.5 - - + +
526C ARG* 4.1 22.0 - - - +
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Residues in contact with ILE 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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491B VAL* 6.0 0.9 - - + -
493B PHE* 3.7 32.3 - - + -
501B MET* 3.0 35.8 + - + +
502B GLY 4.5 1.3 - - - +
503B ILE* 3.5 34.3 - - + -
518B ILE* 4.2 9.0 - - + -
522B GLY 3.3 0.2 - - - -
523B MET* 1.3 75.6 - - - +
525B HIS* 1.3 63.4 + - - +
527B GLN* 3.3 14.3 + - - +
528B GLY* 3.0 19.4 + - - -
529B THR 4.4 1.6 + - - -
530B LEU* 3.9 40.1 + - + +
565B PHE* 5.3 4.5 - - + -
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Residues in contact with HIS 525 (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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502B GLY 5.2 0.4 + - - -
518B ILE* 3.7 20.8 + - + +
519B MET 3.2 22.8 + - - +
520B HIS* 3.2 45.6 + + - +
522B GLY 3.3 3.9 + - - +
523B MET 3.3 0.4 - - - -
524B ILE* 1.3 80.2 - - - +
526B ARG* 1.3 65.1 + - - +
528B GLY* 3.2 14.9 + - - -
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Residues in contact with ARG 526 (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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522B GLY 3.0 16.7 + - - +
523B MET* 3.6 5.2 - - - +
525B HIS* 1.3 82.4 - - - +
527B GLN* 1.3 64.1 + - - +
528B GLY* 3.4 1.0 + - - -
526C ARG* 3.6 24.7 - - - +
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Residues in contact with GLN 527 (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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491B VAL* 3.7 18.0 - - - +
492B GLN 2.8 29.7 + - - -
493B PHE* 4.2 14.5 - - + +
523B MET 3.0 18.0 + - - +
524B ILE* 3.6 19.9 - - - +
526B ARG* 1.3 78.9 - - - +
528B GLY* 1.3 62.1 + - - +
529B THR* 3.4 23.8 + - - +
530B LEU* 4.9 2.8 + - - +
601B EDO 5.0 2.0 + - - -
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Residues in contact with GLY 528 (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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524B ILE 3.0 10.9 + - - -
525B HIS* 3.2 14.6 + - - -
526B ARG 4.2 0.7 - - - -
527B GLN* 1.3 76.2 - - - +
529B THR* 1.3 61.3 + - - +
530B LEU 3.8 5.2 - - - -
531B HIS* 4.5 10.4 + - - -
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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