Contacts of the strand formed by residues 100 - 104 (chain A) in PDB entry 1OZ7
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 CYS 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TRP* 2.8 35.2 - - + -
66A TRP* 3.4 21.1 - - + -
69A LEU 4.0 4.7 - - - -
70A SER* 5.0 1.1 - - - -
98A SER 3.3 2.3 + - - +
99A GLU* 1.3 81.5 - - - +
101A PHE* 1.3 61.4 - - - +
114A ALA* 3.4 6.9 - - - +
115A THR* 2.7 35.5 + - - +
117A CYS* 2.0 44.9 - - - -
77B TRP* 3.7 0.4 - - - -
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Residues in contact with PHE 101 (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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23A TRP* 5.2 0.2 - - - -
66A TRP* 3.1 17.2 - - - -
67A THR* 3.4 19.7 + - - +
69A LEU* 3.5 34.2 + - + +
100A CYS* 1.3 74.4 - - - +
102A VAL* 1.3 59.4 - - - +
112A TRP* 3.6 17.9 - - + -
113A VAL* 3.4 27.1 - - - -
114A ALA* 3.3 17.0 - - + -
115A THR* 4.0 0.2 - - - -
72B TRP* 3.8 36.8 - + - -
77B TRP* 3.6 50.9 - + - -
90B TRP* 4.1 20.6 - + + -
94B ARG* 5.2 0.4 - - - -
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Residues in contact with VAL 102 (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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64A LYS* 4.1 13.7 - - + -
65A ILE 3.0 27.1 - - - +
66A TRP* 3.5 21.5 - - + -
67A THR* 3.8 5.2 - - - -
101A PHE* 1.3 75.4 - - - +
103A LEU* 1.3 63.5 + - - +
112A TRP* 3.5 6.8 - - - +
113A VAL* 3.2 29.2 + - - +
115A THR* 3.8 9.2 - - + -
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Residues in contact with LEU 103 (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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42A ILE* 5.4 4.5 - - + -
48A GLU 5.9 0.2 - - - +
51A VAL* 4.1 24.9 - - + -
52A ASP 5.2 0.7 - - - +
55A VAL* 4.7 7.4 - - + -
63A TYR 3.6 0.2 - - - +
64A LYS* 3.0 10.9 - - - +
65A ILE* 2.6 40.9 + - + +
67A THR* 3.6 28.3 - - + -
102A VAL* 1.3 73.5 - - - +
104A GLU* 1.3 60.5 + - - +
105A LYS 4.0 0.2 + - - -
109A PHE* 3.5 40.9 - - + +
110A ARG 4.9 0.7 - - - -
111A THR 3.7 3.4 - - - +
112A TRP* 3.3 36.3 - - + +
113A VAL* 4.9 0.2 - - - -
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Residues in contact with GLU 104 (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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63A TYR 3.5 7.4 - - - +
64A LYS* 4.4 9.6 + - - +
102A VAL 4.0 0.4 + - - -
103A LEU* 1.3 72.7 - - - +
105A LYS* 1.3 56.6 + - - +
106A GLN* 3.3 24.1 - - + +
107A SER* 3.1 23.3 + - - +
109A PHE* 2.7 29.0 + - - +
111A THR* 2.6 28.3 + - - +
113A VAL* 3.7 33.6 - - + +
94B ARG* 4.9 5.2 + - - -
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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