Contacts of the strand formed by residues 92 - 101 (chain U) in PDB entry 5C3I
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 VAL 92 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88U ASP 5.3 1.9 - - - +
91U GLY* 1.3 74.2 - - - -
93U THR* 1.3 63.4 + - - +
112U TYR* 4.0 21.5 - - + -
113U VAL 3.4 14.8 - - - +
114U ASN* 3.6 12.0 + - + +
110V CYS* 3.7 28.9 - - - +
113V HIS* 3.8 27.6 - - + -
114V ALA* 3.8 25.7 - - + +
116V ARG* 5.3 0.9 - - - +
122V LYS* 5.3 5.0 + - - -
123V ASP* 5.1 0.9 - - - +
126V LEU* 3.7 17.2 - - + +
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Residues in contact with THR 93 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44U TYR* 3.3 37.9 - - + +
45U VAL* 2.8 26.0 + - - +
46U GLY 5.2 1.1 - - - -
47U SER* 5.9 0.3 - - - -
48U ALA 5.8 0.7 + - - -
88U ASP 5.3 5.6 - - - -
92U VAL* 1.3 76.0 - - - +
94U VAL* 1.3 68.6 + - - +
112U TYR* 3.6 4.3 - - - -
113U VAL* 2.7 46.5 + - + +
115U ASN* 3.8 10.3 - - - +
126V LEU* 3.8 13.4 - - - +
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Residues in contact with VAL 94 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44U TYR* 4.9 0.2 - - - -
45U VAL* 3.1 53.5 + - + +
93U THR* 1.3 82.0 + - - +
95U VAL* 1.3 66.2 + - - +
96U LEU* 5.1 1.8 - - + -
111U TYR 3.3 12.1 - - - +
112U TYR* 3.7 24.2 - - + -
126V LEU* 4.0 17.7 - - + +
129V ARG* 3.9 19.3 - - + -
130V ILE* 3.6 30.7 - - + +
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Residues in contact with VAL 95 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22U PHE* 4.1 20.4 - - + -
24U PHE* 4.6 13.7 - - + -
42U ILE* 4.2 19.3 - - + -
43U ILE 3.5 11.0 - - - +
44U TYR* 3.7 28.7 - - + -
57U LEU* 5.7 0.2 - - + -
94U VAL* 1.3 76.1 - - - +
96U LEU* 1.3 67.5 + - - +
97U ILE* 5.3 0.9 - - + -
109U VAL 3.7 0.7 - - - +
110U GLY* 3.4 3.8 - - - -
111U TYR* 2.9 38.4 + - + +
113U VAL* 3.4 26.9 - - + -
139U ILE* 6.2 0.4 - - + -
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Residues in contact with LEU 96 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41U LYS 3.7 1.0 - - - +
42U ILE* 3.3 4.9 - - - +
43U ILE* 2.7 63.1 + - + +
45U VAL* 4.2 23.3 - - + -
94U VAL* 5.1 2.9 - - + -
95U VAL* 1.3 83.8 - - - +
97U ILE* 1.3 62.6 + - - +
98U THR* 4.0 1.5 + - + -
108U ARG* 4.2 39.5 - - + +
109U VAL 3.3 2.0 - - - +
110U GLY* 3.8 17.0 - - - -
129V ARG* 3.3 37.5 - - - +
130V ILE* 4.3 2.0 - - - +
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Residues in contact with ILE 97 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U VAL* 4.0 18.4 - - + -
24U PHE* 3.7 53.6 - - + -
26U ILE* 4.3 21.5 - - + -
40U TRP* 4.4 11.0 - - + -
41U LYS 3.4 8.7 - - - +
42U ILE* 4.2 11.4 - - + -
74U PHE* 5.1 1.1 - - + -
95U VAL* 5.3 1.6 - - + -
96U LEU* 1.3 73.9 - - - +
98U THR* 1.3 65.9 + - - +
107U ILE* 4.0 1.4 - - - +
108U ARG* 3.6 1.0 - - - -
109U VAL* 2.8 48.7 + - + +
111U TYR* 4.0 12.8 - - + -
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Residues in contact with THR 98 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39U GLU 4.4 0.2 - - - -
40U TRP* 3.5 8.4 - - - -
41U LYS* 2.9 56.5 + - - +
43U ILE* 4.0 15.5 - - + +
96U LEU* 4.6 2.7 - - + -
97U ILE* 1.3 76.8 - - - +
99U CYS* 1.3 64.4 + - - +
100U THR* 5.2 3.1 - - - +
105U GLU* 3.3 13.2 - - - +
107U ILE* 3.3 9.0 - - - -
108U ARG* 3.3 43.9 + - + +
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Residues in contact with CYS 99 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U LEU* 4.0 14.4 - - - -
39U GLU 3.2 9.0 - - - -
40U TRP* 3.5 46.2 - - + -
98U THR* 1.3 77.6 - - - +
100U THR* 1.3 66.3 + - - +
105U GLU* 3.6 2.8 - - - +
106U PHE* 3.1 53.8 + - + -
107U ILE* 3.2 16.9 + - + -
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Residues in contact with THR 100 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37U ASP 4.0 0.5 - - - +
38U LEU* 3.4 5.2 - - - +
39U GLU* 2.8 62.9 + - - +
41U LYS* 5.6 7.0 - - + -
98U THR* 5.2 4.3 - - - +
99U CYS* 1.3 78.8 - - - +
101U TYR* 1.3 59.5 + - - +
102U ARG 4.4 0.2 + - - -
103U GLY* 4.2 10.9 + - - +
104U GLN 3.2 19.1 - - - +
105U GLU* 3.5 27.1 - - + +
106U PHE* 4.0 4.3 - - - -
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Residues in contact with TYR 101 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3U LYS* 6.1 2.9 - - + -
34U LEU* 3.6 40.1 - - + +
35U SER* 3.4 30.3 + - - -
36U GLU* 3.4 37.9 + - + -
37U ASP 3.6 13.0 - - - -
38U LEU* 3.7 22.2 - - + -
100U THR* 1.3 72.6 - - - +
102U ARG* 1.3 78.7 + - + +
103U GLY 3.1 0.9 - - - -
104U GLN* 3.0 27.0 + - - +
106U PHE* 4.0 4.5 - - + -
151U ILE* 4.1 12.5 - - + +
152U ASN 4.4 15.7 - - - -
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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