Contacts of the strand formed by residues 44 - 48 (chain A) in PDB entry 1WZN
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 ARG 44 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ARG* 1.3 77.6 - - + +
45A VAL* 1.3 61.6 + - - +
65A GLU* 2.4 53.7 + - + +
67A VAL* 3.7 18.8 - - - +
91A GLU* 4.5 7.7 + - - -
102A PHE* 5.7 1.8 - - - -
105A GLU* 3.6 34.0 + - - +
106A PHE* 3.5 38.0 - - + -
107A ASP* 2.9 41.1 + - - +
108A ALA 3.4 5.2 + - - +
136A LYS* 5.5 4.9 - - - +
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 4.2 9.2 - - + -
42A VAL* 4.0 22.4 - - + -
44A ARG* 1.3 79.0 - - - +
46A LEU* 1.3 72.1 + - - +
47A ASP* 3.9 1.1 - - - +
59A LEU* 4.5 12.8 - - + -
64A TYR* 4.2 21.8 - - + -
65A GLU 2.9 9.2 + - - +
66A VAL* 3.3 13.3 - - + +
67A VAL 2.9 25.3 + - - -
106A PHE* 3.7 5.5 - - - -
108A ALA* 3.3 12.8 - - + +
110A THR* 4.0 24.2 - - + +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 1.3 71.9 - - - +
47A ASP* 1.3 61.0 + - - +
48A LEU* 3.6 31.9 - - + -
67A VAL* 3.4 32.3 - - + +
69A LEU* 4.7 9.0 - - + -
100A ILE* 4.4 6.3 - - + -
102A PHE* 3.7 36.6 - - + -
106A PHE* 3.6 26.4 - - + -
108A ALA 3.0 9.0 + - - +
109A VAL* 3.2 16.3 - - + +
110A THR 2.8 24.9 + - - +
134A ALA* 4.6 2.5 - - + -
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Residues in contact with ASP 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 3.9 2.4 + - + -
46A LEU* 1.3 72.9 - - - +
48A LEU* 1.3 63.1 + - - +
50A CYS* 3.4 16.1 - - + +
55A PRO* 4.3 5.5 - - - +
56A THR* 2.6 37.9 + - + +
59A LEU* 5.5 1.3 - - + -
66A VAL* 4.3 12.8 - - + -
67A VAL 2.8 14.0 + - - +
68A GLY* 3.4 1.4 - - - -
69A LEU 3.0 24.7 + - - -
110A THR* 2.7 29.2 + - - +
112A PHE* 3.3 19.2 + - - +
1001A SAH 4.8 0.9 + - - -
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.6 26.7 - - + -
47A ASP* 1.3 71.1 - - - +
49A ALA* 1.3 74.3 + - - +
50A CYS 3.2 1.8 - - - -
69A LEU* 3.9 25.6 - - + -
97A VAL* 3.7 11.4 - - + -
100A ILE* 4.1 13.2 - - + -
109A VAL* 3.5 30.7 - - + -
110A THR 2.8 12.4 + - - +
111A MET* 3.7 26.6 - - + +
112A PHE 4.5 1.0 + - - -
127A LEU* 4.2 14.8 - - + -
131A VAL* 3.8 20.2 - - + -
141A PHE* 5.0 2.9 - - + -
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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