Contacts of the strand formed by residues 66 - 70 (chain A) in PDB entry 1IZC
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 PHE 66 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.5 39.5 - - + -
44A MET 4.0 0.4 + - - -
45A GLY* 3.2 26.3 - - - -
46A VAL 3.1 26.1 + - - -
64A PRO* 3.1 9.5 - - - +
65A ASP* 1.3 80.7 - - - +
67A VAL* 1.3 67.8 + - - +
68A TRP* 3.8 31.0 - + + -
96A SER 4.4 0.2 - - - -
97A LEU* 3.0 21.5 - - + +
99A ILE* 3.9 25.8 - - + -
251A PHE* 6.1 0.9 - + - -
252A GLY 5.4 0.2 - - - -
270A ALA* 4.2 9.2 - - + -
271A ILE 3.5 29.2 - - - -
272A ALA* 3.8 7.0 - - + -
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 3.5 12.3 - - + +
48A HIS* 3.7 32.5 - - + -
56A THR* 4.7 2.2 - - + -
59A LEU* 4.7 11.0 - - + -
60A ALA* 5.0 3.8 - - - +
64A PRO* 3.9 18.2 - - + -
66A PHE* 1.3 77.5 - - - +
68A TRP* 1.3 60.9 + - - +
69A ILE* 3.7 14.0 + - + -
88A ALA* 4.0 28.5 - - + -
96A SER* 4.2 7.2 - - - -
97A LEU 2.9 6.9 + - - +
98A VAL* 3.5 5.6 - - + +
99A ILE 3.0 24.4 + - - +
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Residues in contact with TRP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL 2.8 15.2 + - - +
47A ALA* 4.1 21.3 - - + -
48A HIS 2.7 31.0 + - - -
66A PHE* 3.8 21.0 - + + -
67A VAL* 1.3 70.0 - - - +
69A ILE* 1.3 58.5 + - - +
70A ASP* 3.6 25.4 - - + -
99A ILE* 3.3 29.1 - - + +
101A ARG* 3.7 49.6 - - + -
122A VAL* 3.8 10.8 - - + +
206A MET* 3.4 41.2 - - + +
251A PHE* 5.5 2.2 - + - -
272A ALA* 5.3 3.8 - - + -
2001A PYR 5.8 3.6 - - + -
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A HIS* 3.6 20.6 - - + +
56A THR* 5.1 0.4 - - + -
67A VAL* 4.0 11.0 - - + -
68A TRP* 1.3 76.1 - - - +
70A ASP* 1.3 62.1 + - - +
71A VAL* 3.6 3.5 + - + -
76A PHE* 3.6 31.2 - - + -
81A LEU* 4.0 17.7 - - + -
84A ALA* 4.2 20.4 - - + +
85A ILE* 3.9 30.3 - - + +
88A ALA* 5.3 0.4 - - + -
98A VAL* 3.9 14.6 - - + -
99A ILE 2.8 11.4 + - - +
100A VAL* 3.3 9.1 - - + +
101A ARG 2.9 24.6 + - - -
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Residues in contact with ASP 70 (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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48A HIS 3.2 13.3 + - - +
49A GLY* 5.0 5.2 - - - -
68A TRP* 3.6 19.9 + - + -
69A ILE* 1.3 69.9 - - - +
71A VAL* 1.3 59.9 + - - +
72A GLU 2.9 15.4 + - - -
73A HIS* 3.2 21.3 + - - +
74A GLY* 2.8 30.9 + - - +
76A PHE* 3.7 7.1 - - - -
101A ARG* 2.9 43.2 + - - +
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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