Contacts of the helix formed by residues 79 - 84 (chain N) in PDB entry 5XVO
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 GLU 79 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4N ARG* 5.8 0.9 - - + -
5N TYR* 3.1 38.1 + - + +
6N MET* 4.1 1.0 - - - +
7N ARG* 2.6 50.8 + - - +
48N ILE* 4.1 8.4 - - - +
77N VAL 3.5 1.6 + - - -
78N THR* 1.3 71.8 - - - +
80N LYS* 1.3 57.4 + - - +
82N PHE* 3.3 5.2 + - - +
83N SER* 2.8 35.9 + - - -
98N ASN 4.4 1.6 - - - +
99N SER* 4.9 0.3 - - - -
100N ASP* 3.5 41.1 - - - +
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Residues in contact with LYS 80 (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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78N THR* 3.0 9.3 - - - +
79N GLU* 1.3 78.9 - - - +
81N GLN* 1.3 61.6 + - - +
83N SER* 2.7 23.7 + - - +
84N ARG* 3.2 32.4 + - - +
21Q T 2.2 59.3 + - - +
22Q A 4.0 22.7 - - - +
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Residues in contact with GLN 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75M LEU* 4.3 7.7 - - + +
76M ASN 3.2 28.3 + - - +
77M VAL* 3.9 3.4 - - - +
78M THR* 4.1 7.7 - - - +
81M GLN* 2.9 40.5 + - - +
77N VAL* 3.5 12.6 - - + +
78N THR* 2.9 43.1 + - - +
80N LYS* 1.3 75.5 - - - +
82N PHE* 1.3 63.5 + - - +
84N ARG* 3.0 22.3 + - - +
85N MET 3.5 4.7 + - - -
22Q A 3.7 19.0 - - - +
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Residues in contact with PHE 82 (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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75M LEU* 4.3 14.4 - - + -
7N ARG* 3.5 62.6 - - + +
9N LEU* 4.4 20.0 - - + -
40N HIS* 4.8 9.6 - + + -
46N SER* 4.2 15.5 - - - -
77N VAL* 4.2 9.8 - - + +
78N THR 3.1 7.3 + - - +
79N GLU* 3.6 7.6 - - - +
81N GLN* 1.3 80.5 - - - +
83N SER* 1.3 63.2 + - - +
85N MET* 3.0 55.3 + - + +
87N TYR* 5.9 0.9 - - - -
98N ASN* 3.9 12.8 - - - -
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Residues in contact with SER 83 (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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79N GLU* 2.8 25.2 + - - -
80N LYS* 2.7 25.3 + - - +
82N PHE* 1.3 77.5 - - - +
84N ARG* 1.3 59.8 + - - +
85N MET* 3.1 8.2 + - - +
100N ASP* 6.1 0.9 - - - -
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Residues in contact with ARG 84 (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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74M LEU 4.7 0.5 - - - +
75M LEU* 5.2 0.6 - - - -
80N LYS* 3.4 33.9 - - - +
81N GLN* 3.0 15.0 + - - +
83N SER* 1.3 79.8 + - - +
85N MET* 1.3 67.1 + - - +
86N ILE* 3.2 14.9 + - - +
21Q T 2.3 42.2 + - - -
22Q A 5.2 3.6 + - - -
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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