Contacts of the strand formed by residues 518 - 522 (chain N) in PDB entry 6NRB
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 VAL 518 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47K MET* 3.5 7.6 - - + -
49K MET* 3.4 45.8 - - + -
59K MET* 3.6 16.8 - - + -
20N LEU* 4.0 14.4 - - - +
23N ASN* 3.6 28.5 - - - +
514N ASN 3.3 20.4 - - - +
515N ILE* 3.1 21.0 + - - +
516N LEU 4.0 2.4 - - - +
517N LEU* 1.3 76.7 - - - +
519N ASP* 1.3 69.9 + - - +
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Residues in contact with ASP 519 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K ILE* 3.6 4.9 - - + -
39K THR* 3.7 2.3 + - - +
46K MET* 3.0 47.9 - - - +
47K MET 3.1 9.5 + - - -
15N ARG* 3.2 32.7 + - - +
16N ALA* 3.0 30.7 + - - +
19N ALA* 3.0 15.8 - - - +
20N LEU* 3.9 3.2 + - - +
116N PRO* 4.0 12.4 - - - +
517N LEU 4.1 0.2 - - - -
518N VAL* 1.3 84.8 - - - +
520N GLU* 1.3 59.7 + - - +
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Residues in contact with GLU 520 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K ILE* 4.3 11.3 - - + +
47K MET 4.4 0.2 + - - -
48K LYS* 3.3 28.8 - - - +
49K MET* 2.7 42.3 + - - +
13N VAL* 3.9 14.7 - - + +
14N ALA 3.1 25.6 + - - +
15N ARG* 3.3 30.9 - - + +
16N ALA 3.9 1.8 - - - +
19N ALA* 3.9 0.2 - - - -
519N ASP* 1.3 75.6 - - - +
521N ILE* 1.3 71.1 + - - +
522N MET* 3.3 14.7 - - - +
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Residues in contact with ILE 521 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K MET* 3.2 30.1 - - + -
51K LEU* 3.5 39.7 - - + +
14N ALA* 2.8 25.1 + - + +
19N ALA* 3.3 25.8 - - + +
22N VAL* 5.2 9.6 - - + -
23N ASN* 5.0 7.2 - - - +
72N PRO* 4.7 15.9 - - + -
520N GLU* 1.3 84.4 - - - +
522N MET* 1.3 62.0 + - - +
523N ARG* 3.4 22.9 + - - +
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Residues in contact with MET 522 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48K LYS* 4.5 11.9 - - - -
49K MET 3.2 8.1 + - - +
50K LEU* 3.1 15.0 - - + +
51K LEU* 2.4 35.0 + - - +
66K ILE* 4.7 2.7 - - + -
67K LEU* 4.4 16.8 - - + -
70K ILE* 3.6 22.9 - - + -
71K GLN 3.6 17.5 - - - +
11N ALA* 3.4 32.5 - - + +
12N GLU 3.4 17.5 - - - +
13N VAL* 5.1 7.6 - - + -
520N GLU* 3.3 17.3 - - - +
521N ILE* 1.3 73.6 - - - +
523N ARG* 1.3 66.4 + - - +
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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