Contacts of the strand formed by residues 91 - 98 (chain C) in PDB entry 3UAJ
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 91 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ARG* 3.9 26.9 - - + -
39C GLN 3.5 16.2 - - - +
40C SER* 3.7 12.1 - - - +
89C ASP 3.0 12.4 + - - +
90C THR* 1.3 75.5 - - - +
92C LEU* 1.3 60.0 + - - +
93C TYR* 3.3 12.9 - - + -
118C LYS* 4.9 0.9 - - - -
119C VAL 3.1 26.4 + - - -
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Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 3.5 2.3 - - - -
39C GLN* 2.8 47.8 + - + +
91C ALA* 1.3 68.0 - - - +
93C TYR* 1.3 59.1 + - - +
94C TYR* 3.3 39.5 + - + +
115C GLN 5.3 0.7 - - - +
116C GLY* 3.6 9.2 - - - +
117C THR 3.6 35.4 - - - +
118C LYS* 3.7 28.7 - - + +
42D GLY 5.9 2.7 - - - +
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Residues in contact with TYR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C GLU* 3.7 2.6 - - - +
18C LEU* 4.1 11.4 - - + +
20C LEU* 3.8 16.4 - - + -
36C TRP* 3.9 8.7 - + + -
37C LEU 3.5 1.8 - - - -
38C ARG* 3.5 35.4 + - + -
48C ILE* 3.7 26.0 - - + -
80C LEU* 3.9 19.1 - - + -
82C LEU* 3.9 10.9 - - + +
89C ASP* 2.9 30.8 + - - +
91C ALA* 3.3 21.3 - - + -
92C LEU* 1.3 70.6 - - - +
94C TYR* 1.3 60.1 + - - +
116C GLY* 3.4 2.6 - - - -
117C THR* 2.8 43.0 + - + +
119C VAL* 3.7 24.9 - - + -
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Residues in contact with TYR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C GLU* 3.4 2.7 - - - -
36C TRP* 3.3 8.6 - - - -
37C LEU* 2.6 44.3 + - + +
39C GLN* 3.9 20.8 + - + -
45C LEU* 4.9 4.0 - - + -
92C LEU* 3.3 42.3 - - + +
93C TYR* 1.3 73.5 - - - +
95C CYS* 1.3 59.1 + - - +
96C ALA 4.2 0.2 - - - -
113C TRP* 3.8 35.7 - + + -
114C GLY 3.7 11.9 - - - -
115C GLN 3.6 20.0 + - - -
116C GLY* 3.7 13.0 - - - -
39D GLN* 3.6 17.3 + - - -
42D GLY 4.8 3.5 + - - -
43D LYS 3.9 5.2 + - - -
44D ALA* 3.8 26.4 + - + -
45D PRO* 4.4 2.5 - - + -
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Residues in contact with CYS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 3.4 13.1 - - - +
6C GLU* 3.2 29.9 + - - -
22C CYS* 2.0 55.0 - - + -
34C TRP* 6.3 1.1 - - + -
35C SER 3.4 6.1 - - - +
36C TRP* 4.0 17.0 - - + +
78C ILE* 5.5 1.6 - - + -
94C TYR* 1.3 73.0 - - - +
96C ALA* 1.3 58.9 + - - +
114C GLY 3.0 23.3 + - - -
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 4.3 0.9 - - - -
34C TRP* 3.7 7.6 - - - +
35C SER* 2.7 43.0 + - - +
37C LEU* 3.9 17.5 - - + -
94C TYR 4.2 0.6 - - - -
95C CYS* 1.3 73.9 - - - +
97C ARG* 1.3 59.4 + - - +
98C GLN 3.5 0.9 + - - -
110C PHE* 3.8 24.5 - - + -
112C LEU 3.3 12.8 - - - +
113C TRP* 4.0 15.0 - - + -
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Residues in contact with ARG 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C VAL* 4.6 9.5 - - - +
4C LEU* 4.5 0.6 - - - +
32C PHE* 3.4 60.0 - - + -
33C TYR 3.6 5.2 - - - +
34C TRP* 3.7 26.6 - - + -
96C ALA* 1.3 67.7 - - - +
98C GLN* 1.3 65.8 + - - +
99C GLY 3.5 1.7 + - - -
103C THR 6.3 0.2 - - - -
104C GLY* 3.4 23.0 + - - +
110C PHE* 3.4 20.9 - - - -
111C ASP* 2.8 37.2 + - - +
112C LEU* 3.0 43.5 + - + +
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Residues in contact with GLN 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B LYS* 4.0 7.0 - - - +
33C TYR* 2.8 40.2 + - + +
35C SER* 3.4 14.8 - - - -
47C TRP* 3.0 27.9 + - - -
50C TYR* 3.4 21.7 - - + +
96C ALA 3.5 3.4 + - - -
97C ARG* 1.3 73.1 - - - +
99C GLY* 1.3 66.4 + - - +
100C THR* 4.2 2.3 - - - +
103C THR* 4.9 1.7 + - - -
108C ASP* 2.8 36.4 + - - +
110C PHE* 3.5 20.8 - - + -
95D TYR* 3.0 14.3 + - - -
97D LEU* 3.9 7.2 - - - -
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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