Contacts of the strand formed by residues 70 - 77 (chain E) in PDB entry 2CVL
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 70 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MSE 4.1 10.9 - - - +
60E LEU* 3.4 32.8 - - + -
66E GLY 3.8 2.0 - - - +
67E LEU* 3.1 18.9 + - - +
68E SER 4.6 0.9 - - - +
69E ARG* 1.3 77.0 - - - +
71E VAL* 1.3 62.0 + - - +
72E GLN 3.7 4.7 - - - +
73E THR* 3.6 31.2 - - + -
94E PHE* 3.9 11.7 - - + -
97E PRO 5.3 0.5 - - - +
98E TYR 5.0 0.2 - - - -
99E PRO* 3.3 22.9 - - + +
119E CYS* 3.9 8.1 - - + -
120E VAL 3.7 7.9 - - - +
121E ALA* 3.6 12.3 - - + -
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Residues in contact with VAL 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MSE 4.5 4.7 - - + -
20D VAL* 3.8 25.0 - - + +
22D ALA* 3.5 25.6 - - + -
27D PHE* 3.6 35.8 - - + +
25E PHE* 4.5 3.1 - - + -
69E ARG 3.6 13.7 - - - +
70E VAL* 1.3 74.4 - - - +
72E GLN* 1.3 62.4 + - + +
99E PRO* 3.9 1.3 - - - -
100E ALA* 2.9 27.8 + - - +
120E VAL* 2.9 27.7 + - + +
121E ALA* 4.5 1.3 - - - -
122E LEU* 4.0 12.3 - - + -
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Residues in contact with GLN 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE* 3.7 35.8 - - + +
28D VAL 5.5 2.8 + - - +
72D GLN* 5.1 2.2 + - - -
118D ALA* 6.1 3.0 - - - +
119D CYS 4.9 3.6 + - - +
120D VAL* 3.8 17.0 - - - +
70E VAL* 3.7 2.2 - - - +
71E VAL* 1.3 84.1 - - + +
73E THR* 1.3 73.3 + - - +
74E THR* 4.3 13.4 + - - -
100E ALA* 3.3 13.0 - - + +
101E ARG* 5.6 0.2 - - - -
119E CYS* 3.1 6.8 - - - +
120E VAL* 2.8 53.7 + - + +
72F GLN* 5.1 2.3 + - - -
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Residues in contact with THR 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E LEU* 6.0 0.9 - - + -
70E VAL* 3.6 20.2 - - + -
72E GLN* 1.3 83.9 - - - +
74E THR* 1.3 64.9 + - - +
75E CYS* 3.6 10.8 - - - -
90E TYR* 2.8 33.2 + - + +
94E PHE* 4.4 6.5 - - + -
99E PRO* 4.1 3.6 - - + -
100E ALA 3.0 6.5 + - - -
101E ARG* 3.2 19.2 - - - +
102E ALA* 3.3 20.3 + - - +
117E VAL* 4.4 5.6 - - + -
118E ALA 3.3 7.9 - - - -
119E CYS* 3.9 7.0 - - + +
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Residues in contact with THR 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D THR* 6.2 2.2 - - + -
76D PHE* 5.5 6.7 - - + -
72E GLN* 4.3 14.7 + - - -
73E THR* 1.3 74.9 + - - +
75E CYS* 1.3 61.1 + - - +
76E PHE* 3.4 36.3 - - + -
102E ALA* 3.7 13.4 - - + +
116E GLU 3.9 1.0 - - - +
117E VAL* 3.5 2.3 - - - -
118E ALA* 2.9 41.9 + - + +
119E CYS* 4.8 0.7 - - - +
74F THR* 6.1 3.1 - - + -
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Residues in contact with CYS 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E THR* 3.6 22.9 - - - -
74E THR* 1.3 76.8 - - - +
76E PHE* 1.3 67.1 + - - +
86E PHE* 3.6 34.8 - - + -
90E TYR* 4.0 4.9 - - - -
101E ARG* 3.8 15.3 - - - -
102E ALA 2.8 13.0 + - - +
103E THR* 3.3 12.7 - - + +
104E VAL* 3.0 24.8 + - - +
116E GLU 3.6 3.8 - - - -
117E VAL* 3.9 13.9 - - + -
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Residues in contact with PHE 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PHE* 4.3 22.0 - + - -
74E THR* 3.4 36.3 - - + -
75E CYS* 1.3 80.3 - - - +
77E LEU* 1.3 66.8 + - - +
104E VAL* 3.3 9.4 - - + +
106E VAL* 3.5 24.9 - - + -
109E LEU* 3.7 21.0 - - + +
115E VAL* 3.3 5.7 - - - +
116E GLU* 2.8 48.3 + - + +
118E ALA* 5.8 1.3 - - + -
74F THR* 5.6 3.6 - - + -
76F PHE* 4.4 13.0 - + - -
102F ALA* 4.9 14.1 - - + -
104F VAL* 3.8 32.5 - - + -
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Residues in contact with LEU 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ILE* 3.8 22.2 - - + -
76E PHE* 1.3 81.5 - - - +
78E ALA* 1.3 61.0 + - - +
79E ASP 3.9 14.8 - - - +
80E MSE 5.1 2.0 - - - +
82E ASP* 4.1 1.6 - - + -
83E PHE* 3.6 50.3 - - + +
86E PHE* 3.9 17.7 - - + -
103E THR* 4.3 14.6 - - + -
104E VAL 3.0 8.9 + - - +
105E ALA* 3.1 9.1 - - + -
106E VAL* 2.8 27.1 + - - +
109E LEU* 4.2 2.9 - - - -
114E ARG 3.4 11.4 - - - +
115E VAL* 3.9 6.7 - - + -
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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