Contacts of the strand formed by residues 68 - 73 (chain A) in PDB entry 3OTC
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 ILE 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 3.9 35.9 - - + +
62A MET* 3.7 35.8 + - + +
65A LEU* 4.2 6.7 - - + -
66A GLU 3.3 2.8 - - - +
67A ASP* 1.3 77.3 - - - +
69A VAL* 1.3 53.4 + - - +
70A ILE 4.0 10.8 - - - +
80A PHE* 4.3 12.8 - - + -
81A VAL 3.3 14.6 - - - +
82A PHE* 3.5 39.7 - - + -
83A LYS* 5.9 0.2 - - - -
214A TRP* 2.6 33.3 + - - -
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 4.2 13.2 - - + -
62A MET* 4.3 2.4 - - - +
67A ASP 3.6 0.2 + - - -
68A ILE* 1.3 75.4 - - - +
70A ILE* 1.3 64.3 + - + +
81A VAL* 2.9 26.9 + - + +
83A LYS* 3.6 37.5 - - + +
140A LEU* 6.3 0.2 - - + -
212A LEU 4.1 4.7 - - - +
213A ILE* 4.2 8.3 - - - +
214A TRP* 3.8 19.6 + - + +
263A GLU 5.8 0.4 - - - +
264A ILE* 3.9 36.2 - - + +
267A GLU* 5.7 5.2 - - + -
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A MET* 4.7 0.9 - - - -
68A ILE* 4.0 3.0 - - - +
69A VAL* 1.3 85.4 - - + +
71A ALA* 1.3 69.7 + - - +
72A TYR* 6.1 0.4 - - + -
81A VAL* 3.0 52.4 + - + +
140A LEU* 5.6 2.7 - - + -
144A LEU* 4.5 19.7 - - + -
211A VAL* 3.9 23.3 - - + -
212A LEU 3.4 12.1 - - - +
213A ILE* 4.2 6.5 - - + -
252A ILE* 5.4 3.6 - - + -
257A PHE* 4.0 20.4 - - + -
258A TRP* 4.1 17.5 - - + -
264A ILE* 4.3 13.2 - - + -
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Residues in contact with ALA 71 (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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62A MET* 3.7 25.6 - - - -
68A ILE* 4.8 0.4 - - + -
70A ILE* 1.3 81.2 - - - +
72A TYR* 1.3 61.9 + - - +
78A TYR* 4.2 3.4 - - + -
79A SER 3.2 14.8 - - - +
80A PHE* 4.0 16.4 - - + -
81A VAL* 5.7 0.4 - - - -
210A THR 3.9 0.5 - - - +
211A VAL* 3.6 2.3 - - - -
212A LEU* 2.9 45.3 + - + +
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Residues in contact with TYR 72 (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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70A ILE* 5.8 0.7 - - + -
71A ALA* 1.3 73.1 - - - +
73A GLY* 1.3 56.3 + - - +
74A GLN* 4.0 17.9 - - + -
77A GLU* 5.0 2.0 - - - +
78A TYR* 3.4 3.5 - - - -
79A SER* 2.7 40.7 + - - -
144A LEU* 4.0 25.1 - - + +
147A ARG* 3.7 41.3 - - + -
148A GLN* 3.3 29.2 - - + +
151A CYS* 3.5 12.0 - - - +
208A LYS 2.6 30.7 + - - -
209A GLY* 3.8 1.9 - - - -
210A THR 2.9 29.4 - - - -
211A VAL* 3.7 16.8 - - + -
252A ILE* 4.1 8.5 - - + -
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Residues in contact with GLY 73 (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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51A LEU* 5.8 1.8 - - - +
72A TYR* 1.3 78.0 - - - +
74A GLN* 1.3 60.6 + - - +
77A GLU* 3.3 16.4 - - - -
78A TYR* 3.3 23.7 - - - -
209A GLY* 4.1 0.5 - - - -
210A THR* 3.2 34.9 + - - +
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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