Contacts of the strand formed by residues 129 - 135 (chain B) in PDB entry 5CVE
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 TYR 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B CYS* 3.7 17.0 - - - +
65B ALA 3.7 18.2 - - - -
66B LEU* 3.7 38.3 - - + +
88B ASP* 2.6 38.2 + - + +
112B ARG* 3.9 3.2 + - - -
115B PHE* 3.9 9.0 - - - -
122B PHE* 5.0 1.9 - - - -
124B PRO* 3.8 16.5 - - + +
125B GLU* 4.7 2.7 + - - +
128B SER* 1.3 97.4 - - - +
130B ASP* 1.3 61.9 + - - +
131B VAL 3.9 5.4 - - - +
132B ILE* 3.8 18.6 - - + -
156B SER* 3.0 21.8 + - - +
157B LEU* 3.4 9.7 - - - +
158B ARG* 2.9 28.1 + - - +
161B GLY* 4.4 0.2 - - - -
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Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B THR* 3.4 5.5 - - + +
61B GLY* 3.2 38.1 + - - +
63B SER* 2.6 42.6 + - - -
64B CYS 2.8 13.5 + - - +
84B PHE* 4.3 2.9 - - + -
129B TYR* 1.3 73.9 - - - +
131B VAL* 1.3 64.7 + - - +
157B LEU* 4.7 0.2 - - - -
158B ARG* 3.5 21.3 - - - +
159B PRO 4.7 3.3 - - - +
161B GLY* 3.1 9.4 - - - -
162B ILE 2.9 25.3 + - - -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 4.4 15.0 - - + -
53B LEU* 5.2 0.7 - - + -
60B THR* 3.8 13.7 - - + -
64B CYS 3.5 2.2 + - - -
65B ALA* 3.1 6.4 - - + +
66B LEU 2.9 23.9 + - - +
80B LEU* 4.9 5.4 - - + -
84B PHE* 3.4 34.3 - - + -
129B TYR* 3.9 1.4 - - - +
130B ASP* 1.3 85.3 - - - +
132B ILE* 1.3 75.5 + - - +
133B TRP* 4.1 24.9 - - + +
162B ILE* 3.3 17.5 - - + +
164B VAL* 4.8 1.3 - - + -
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 3.5 10.5 - - + -
68B CYS* 3.8 26.0 - - - -
129B TYR* 3.8 20.6 - - + -
131B VAL* 1.3 75.3 - - - +
133B TRP* 1.3 55.1 + - - +
134B ILE* 4.0 8.5 - - + -
153B CYS* 3.4 39.7 - - + +
156B SER* 3.1 27.1 - - - +
157B LEU* 3.6 15.0 - - + -
162B ILE 3.0 6.5 + - - -
163B ILE* 3.3 10.4 - - + +
164B VAL 2.8 33.3 + - - +
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Residues in contact with TRP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER* 3.4 44.0 - - - -
48B PHE* 4.7 6.5 - + - -
49B LEU* 3.9 19.3 - - + -
66B LEU 2.8 13.4 + - - +
67B ASP* 3.7 6.3 - - - +
68B CYS* 2.8 32.3 + - - +
75B ILE* 3.9 20.9 - - + +
79B LEU* 3.6 17.9 - - + -
80B LEU* 4.2 18.6 - - + -
131B VAL* 4.0 13.6 - - + -
132B ILE* 1.3 70.7 - - - +
134B ILE* 1.3 60.0 + - - +
135B GLN* 2.8 36.5 + - + +
164B VAL* 3.6 46.0 - - + -
166B LYS* 4.4 7.8 - - + +
219B SER* 5.7 0.4 - - - -
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B CYS* 3.9 21.5 - - + -
119B LEU* 4.7 6.1 - - + -
132B ILE* 4.0 9.6 - - + +
133B TRP* 1.3 76.8 - - - +
135B GLN* 1.3 59.3 + - - +
137B VAL* 3.6 23.1 - - + -
138B ILE* 3.7 21.2 - - + +
146B LEU* 5.9 0.7 - - + -
149B PHE* 3.9 15.5 - - + -
150B LEU* 3.7 30.7 - - + -
153B CYS* 4.4 1.6 - - - -
163B ILE* 3.7 17.5 - - + -
164B VAL 2.8 13.3 + - - +
165B ILE* 3.3 9.1 - - + +
166B LYS 2.9 23.4 + - - +
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASP* 2.8 30.6 + - - +
45B SER* 4.1 1.6 + - - -
68B CYS 3.9 6.9 + - - -
74B ARG* 3.7 0.4 - - - +
75B ILE* 3.4 23.4 - - + +
133B TRP* 2.8 38.7 + - - +
134B ILE* 1.3 75.6 - - - +
136B TRP* 1.3 99.0 + - + +
137B VAL* 3.3 6.4 + - - +
166B LYS* 3.1 32.5 - - + +
301B SAH 2.7 28.3 + - - +
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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