Contacts of the strand formed by residues 140 - 148 (chain R) in PDB entry 5A0Q
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 GLY 140 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39R ASP 5.0 3.3 - - - +
136R PHE* 3.3 21.6 - - - -
137R ASP* 3.0 29.2 + - - +
141R THR* 1.3 67.6 + - - +
142R PRO* 3.9 2.9 - - - +
213R ARG* 3.3 42.9 - - - +
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Residues in contact with THR 141 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R ARG* 4.5 8.5 - - - +
136R PHE* 3.8 1.2 - - - -
137R ASP* 2.8 41.1 + - - +
140R GLY* 1.3 79.6 + - - +
142R PRO* 1.3 80.8 - - + +
143R ARG* 3.8 3.9 + - - -
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Residues in contact with PRO 142 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R ARG* 2.9 55.6 - - + +
37R GLY 3.3 22.9 - - - +
38R ARG 4.3 11.7 - - - +
39R ASP 5.2 2.0 - - - +
40R ILE* 5.1 0.2 - - - -
41R VAL* 3.4 25.8 - - + +
135R GLY 4.1 2.5 - - - +
136R PHE* 4.8 7.1 - - + -
140R GLY 3.9 5.6 - - - +
141R THR* 1.3 94.4 - - + +
143R ARG* 1.4 68.6 + - - +
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Residues in contact with ARG 143 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R ARG* 4.2 4.3 - - - +
41R VAL* 4.2 1.4 - - - +
104R VAL* 4.5 3.3 - - + +
105R GLU* 3.6 18.1 + - - +
134R VAL* 3.4 8.1 - - - +
135R GLY 3.2 31.5 + - - +
137R ASP* 3.1 38.3 + - - +
141R THR* 3.9 5.4 - - - +
142R PRO* 1.4 86.3 - - - +
144R LEU* 1.3 61.2 + - - +
145R TYR* 3.2 45.5 + - + -
155R ALA* 3.9 10.3 - - - +
156R TRP 5.4 2.0 + - - -
60S GLU* 5.3 4.9 - - - +
63S SER* 3.3 21.4 + - - -
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Residues in contact with LEU 144 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34R GLY* 3.4 7.0 - - - -
35R VAL* 3.0 48.9 - - - +
36R ARG* 3.4 16.3 - - + +
41R VAL* 5.7 0.2 - - + -
42R VAL 4.4 1.8 - - - +
132R LEU* 4.5 7.4 - - + -
133R ILE 4.0 3.1 - - - -
134R VAL* 4.0 22.4 - - + -
143R ARG* 1.3 74.4 - - - +
145R TYR* 1.3 64.1 + - - +
155R ALA* 4.8 0.2 - - - -
156R TRP* 2.9 49.9 + - + +
158R ALA 4.2 2.0 - - - +
159R ASN* 4.0 22.0 - - + +
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Residues in contact with TYR 145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104R VAL* 4.6 6.5 - - + -
105R GLU* 3.2 34.9 - - + +
108R THR* 3.6 31.2 - - + +
132R LEU* 3.5 17.3 - - - +
133R ILE* 3.1 24.1 + - + +
143R ARG* 3.2 50.0 + - + -
144R LEU* 1.3 79.3 - - - +
146R GLN* 1.3 57.6 + - - +
153R TYR* 3.7 30.4 - + - -
154R HIS 3.5 16.4 - - - -
155R ALA* 3.5 18.2 - - + +
156R TRP* 4.4 0.9 - - - -
159R ASN* 5.3 0.2 + - - -
63S SER* 3.8 6.7 + - - -
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Residues in contact with GLN 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131R ALA 3.7 5.2 - - - -
132R LEU* 4.8 0.2 - - - +
145R TYR* 1.3 73.7 - - - +
147R THR* 1.3 71.9 + - - +
148R ASP* 4.7 18.8 + - - +
152R THR* 5.1 1.2 + - - +
153R TYR* 3.3 5.2 - - - +
154R HIS* 2.9 53.8 + - - +
156R TRP* 3.3 32.5 - - - +
159R ASN* 3.2 29.6 + - - +
161R ILE* 4.1 14.1 - - + +
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Residues in contact with THR 147 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108R THR* 3.5 19.1 - - - +
111R ILE* 4.4 1.3 - - + -
112R ALA* 3.8 36.1 - - + +
115R LYS* 3.7 24.5 - - + +
130R SER* 3.1 26.9 - - - -
131R ALA* 3.0 11.3 + - - -
133R ILE* 3.5 15.3 - - - +
146R GLN* 1.3 77.7 + - - +
148R ASP* 1.4 65.1 + - - +
152R THR 3.5 11.0 - - - +
153R TYR* 4.3 0.9 - - + -
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Residues in contact with ASP 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23R GLN* 4.2 13.8 + - - +
115R LYS* 3.7 8.6 - - - +
129R ILE 4.3 2.2 - - - -
130R SER* 3.7 7.0 - - - +
146R GLN* 4.7 16.9 + - - +
147R THR* 1.4 74.4 - - - +
149R PRO* 1.3 74.3 - - + +
150R SER* 3.4 15.9 + - - -
151R GLY* 3.1 11.4 + - - -
152R THR* 3.1 43.6 + - - +
154R HIS* 5.8 0.5 + - - -
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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