Contacts of the strand formed by residues 88 - 94 (chain A) in PDB entry 4UU9
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ARG* 3.9 10.3 - - + -
39A GLN 3.4 29.8 - - - +
40A ALA* 3.7 5.2 - - + +
41A PRO* 4.4 4.3 - - - -
86A ASP 3.2 5.2 + - - +
87A THR* 1.3 77.5 - - - +
89A VAL* 1.3 57.8 + - - +
90A TYR* 3.4 21.1 - - + -
108A MET* 3.7 7.0 - - - -
109A VAL 2.8 34.8 + - - +
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Residues in contact with VAL 89 (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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37A VAL 4.1 0.2 - - - +
38A ARG* 3.2 2.9 - - - -
39A GLN* 2.9 40.8 + - + +
41A PRO* 5.1 3.1 - - + +
88A ALA* 1.3 72.1 - - - +
90A TYR* 1.3 60.5 + - - +
91A TYR* 3.6 35.3 + - + +
105A GLN 4.9 1.1 - - - +
106A GLY* 3.8 21.3 - - - -
107A THR 3.5 4.7 - - - +
108A MET* 3.6 24.0 - - + -
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Residues in contact with TYR 90 (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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6A GLU* 3.8 4.2 - - - +
20A LEU* 3.6 28.0 - - + -
36A TRP* 4.4 7.2 - + + -
37A VAL 3.7 3.6 - - - -
38A ARG* 3.0 40.3 + - + +
48A VAL* 4.3 10.5 - - + -
67A PHE* 4.1 10.7 - + - -
80A LEU* 4.3 9.9 - - + -
82A MET* 4.0 16.8 + - - -
86A ASP* 2.7 35.6 + - - +
88A ALA* 3.4 22.7 - - + -
89A VAL* 1.3 73.0 - - - +
91A TYR* 1.3 62.1 + - - +
106A GLY* 3.3 1.0 - - - -
107A THR* 2.8 41.4 + - - +
109A VAL* 3.4 20.8 - - + +
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Residues in contact with TYR 91 (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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6A GLU* 3.2 4.5 - - - +
36A TRP* 3.3 9.3 - - - -
37A VAL* 2.7 45.0 + - - +
39A GLN* 3.7 25.6 + - + -
45A LEU* 4.7 4.7 - - + -
89A VAL* 3.6 24.7 - - + +
90A TYR* 1.3 72.8 - - - +
92A CYS* 1.3 59.6 + - - +
103A TRP* 3.8 31.4 - + + -
104A GLY 3.9 10.3 - - - -
105A GLN 3.6 20.2 + - - -
106A GLY* 3.4 17.3 - - - -
38B GLN* 3.6 14.7 + - - -
41B GLY 5.8 0.3 - - - -
42B LYS 3.7 8.1 + - - -
43B ALA* 3.6 17.7 - - + -
44B PRO* 3.9 11.9 - - + -
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Residues in contact with CYS 92 (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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4A LEU* 3.7 14.3 - - - +
5A LEU 4.7 0.2 - - - -
6A GLU* 2.9 25.1 + - - +
22A CYS* 2.1 53.4 - - + -
34A MET* 4.9 0.7 - - + -
35A SER 3.3 4.7 - - - -
36A TRP* 3.9 7.6 - - + -
78A LEU* 3.9 16.2 - - + -
91A TYR* 1.3 75.8 - - - +
93A ALA* 1.3 61.5 + - - +
103A TRP* 3.7 0.5 - - - -
104A GLY 3.0 25.8 + - - -
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Residues in contact with ALA 93 (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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4A LEU* 3.9 1.1 - - - -
34A MET* 3.5 11.7 - - - +
35A SER* 2.9 35.0 + - - +
37A VAL* 5.2 1.6 - - + -
92A CYS* 1.3 76.9 - - - +
94A ARG* 1.3 61.0 + - - +
95A ASP* 4.9 0.2 - - - -
100A MET* 3.8 31.4 - - - -
102A VAL 3.1 12.3 - - - +
103A TRP* 3.9 19.3 - - + -
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Residues in contact with ARG 94 (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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2A VAL* 4.2 8.5 - - - +
4A LEU* 3.8 4.2 - - + +
27A PHE* 3.5 43.5 - - + +
32A TYR* 3.4 54.2 + - + -
34A MET* 3.8 15.3 - - + -
93A ALA* 1.3 70.5 - - - +
95A ASP* 1.3 60.5 + - - +
100A MET* 3.1 5.4 - - - +
101A ASP* 2.6 67.5 + - - +
102A VAL* 2.8 33.2 + - + +
14C LYS 3.6 13.1 + - - -
16C SER* 3.7 10.1 + - - +
19C LYS* 5.2 5.1 - - - +
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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