Contacts of the strand formed by residues 67 - 72 (chain L) in PDB entry 2VWE
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 ALA 67 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48L ILE* 3.6 31.4 - - + -
59L TYR* 3.2 29.7 - - + -
63L PHE* 3.8 10.6 + - + +
64L LYS 5.3 1.0 - - - +
65L ARG* 4.6 1.7 - - - -
66L MET* 1.3 83.8 + - + +
68L THR* 1.3 63.6 + - - +
80L MET* 3.8 15.9 - - + -
81L GLN 3.5 2.0 - - - -
82L LEU* 4.2 5.6 - - + -
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Residues in contact with THR 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L TYR* 3.7 10.3 - - + +
65L ARG 5.1 4.5 + - - -
67L ALA* 1.3 76.7 + - - +
69L LEU* 1.3 70.2 + - - +
70L THR* 4.0 10.2 + - + -
79L TYR 4.0 0.5 - - - +
80L MET* 3.5 2.1 - - - -
81L GLN* 2.6 59.1 + - + +
82L SER* 4.3 8.1 - - - +
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Residues in contact with LEU 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L TRP* 3.4 26.2 - - + +
49L GLY* 3.6 20.0 - - - +
50L HIS* 3.5 34.1 - - - +
51L ILE* 3.4 27.5 - - + +
57L THR* 4.2 3.6 + - - +
58L ASN 4.3 0.2 - - - +
59L TYR* 2.9 36.7 + - + +
68L THR* 1.3 74.0 - - - +
70L THR* 1.3 66.3 + - - +
79L TYR 3.5 11.9 - - - +
80L MET* 3.7 24.9 - - + -
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Residues in contact with THR 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L LYS* 4.3 10.2 - - - -
51L ILE* 3.9 3.6 - - - +
68L THR* 4.0 13.4 + - + +
69L LEU* 1.3 78.5 - - - +
71L VAL* 1.3 67.0 + - - +
78L ALA* 3.6 0.5 - - - +
79L TYR* 2.6 59.3 + - - +
81L GLN* 5.6 2.8 + - + +
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Residues in contact with VAL 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L PHE* 4.0 13.9 - - + -
34L ILE* 5.3 0.2 - - + -
51L ILE* 3.9 28.0 - - + -
52L PRO* 3.8 45.1 - - + +
55L GLY* 5.5 6.3 - - - -
70L THR* 1.3 82.0 - - - +
72L ASP* 1.3 63.8 + - - +
73L LYS* 4.4 3.5 + - + +
77L THR 3.6 4.3 - - - +
78L ALA* 4.0 9.9 - - + -
79L TYR* 4.7 2.9 - - - -
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Residues in contact with ASP 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L PHE* 3.9 6.0 - - - -
71L VAL* 1.3 76.2 - - - +
73L LYS* 1.3 67.6 + - - +
74L SER* 3.1 35.8 + - - +
75L SER* 4.5 5.0 - - - -
76L SER* 3.5 3.8 - - - -
77L THR* 2.9 33.0 + - - +
79L TYR* 4.1 18.0 + - + -
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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