Contacts of the strand formed by residues 65 - 69 (chain A) in PDB entry 5ITZ
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 65 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER 3.1 10.5 - - - +
8A HIS* 4.2 1.1 - - - +
21A TRP* 3.8 31.2 - - + +
63A PRO* 3.0 15.4 + - + -
64A ARG* 1.3 75.7 - - - +
66A VAL* 1.3 65.2 + - - +
67A PHE* 4.1 16.3 - - + -
87A PHE* 4.4 0.7 - - + -
91A GLN* 2.5 38.1 + - - +
125A LEU* 3.6 2.4 - - - +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.4 7.4 - - + -
6A SER 2.8 6.5 + - - +
7A ILE* 3.4 11.0 - - + -
8A HIS* 2.8 31.2 + - - -
65A ALA* 1.3 77.4 - - - +
67A PHE* 1.3 64.7 + - - +
68A VAL* 3.9 12.1 - - + -
91A GLN* 3.4 15.9 - - + +
93A ILE* 3.7 24.5 - - + -
118A VAL* 5.0 0.4 - - + -
121A ARG* 4.9 4.5 - - + +
122A ILE* 3.9 29.8 - - + +
125A LEU* 3.5 22.0 - - + -
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Residues in contact with PHE 67 (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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8A HIS* 3.5 32.1 - + + -
14A VAL* 3.6 34.3 - - + -
17A GLY 4.3 1.6 - - - -
18A ASN* 3.5 22.4 - - - -
21A TRP* 4.1 7.2 - + - -
65A ALA* 4.1 6.3 - - + -
66A VAL* 1.3 77.2 - - - +
68A VAL* 1.3 58.8 + - - +
75A ILE* 3.5 14.8 - - + -
78A VAL* 5.0 4.3 - - + -
87A PHE* 3.4 44.2 - + - -
91A GLN 2.9 7.9 + - - +
92A LEU* 3.5 28.7 - - + -
93A ILE* 2.7 35.0 + - - +
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.7 9.0 - - + -
8A HIS 2.8 14.7 + - - +
9A VAL* 3.4 5.8 - - + +
10A GLY 2.9 24.1 + - - -
14A VAL* 4.2 1.4 - - - +
66A VAL* 3.9 14.6 - - + -
67A PHE* 1.3 78.8 - - - +
69A ASP* 1.3 70.9 + - - +
70A LEU* 5.3 1.6 - - + -
75A ILE* 3.7 2.2 - - - +
93A ILE* 3.3 13.2 - - + +
114A ILE* 5.1 5.8 - - + -
118A VAL* 3.7 44.6 - - + -
145A THR* 5.8 0.4 - - + -
149A PHE* 3.8 23.3 - - + -
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Residues in contact with ASP 69 (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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10A GLY* 3.5 22.4 - - - +
11A GLN* 3.7 12.1 + - - -
14A VAL* 4.7 1.5 - - + +
68A VAL* 1.3 77.9 - - - +
70A LEU* 1.3 73.7 + - - +
71A GLU* 3.3 31.9 + - - +
74A VAL* 4.0 15.1 - - - +
75A ILE* 3.8 16.8 - - + -
93A ILE 3.0 6.1 + - - +
94A THR* 3.2 7.4 - - - -
95A GLY 3.0 19.9 + - - -
114A ILE* 4.7 0.5 - - - +
145A THR* 4.0 8.6 + - - +
501A GTP 3.8 7.3 + - - -
502A MG 4.1 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