Contacts of the strand formed by residues 70 - 77 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MSE 2.8 20.5 - - - +
60C LEU* 3.5 32.1 - - + -
66C GLY 3.7 1.8 - - - +
67C LEU 3.1 17.0 + - - +
69C ARG* 1.3 76.8 - - - +
71C VAL* 1.3 59.3 - - - +
72C GLN 3.6 10.8 - - - +
73C THR* 3.6 31.0 - - + -
94C PHE* 3.5 13.9 - - + -
99C PRO* 3.4 20.0 - - + +
119C CYS* 4.0 8.3 - - + -
120C VAL 3.7 2.9 - - - +
121C ALA* 3.6 11.7 - - + -
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Residues in contact with VAL 71 (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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1B MSE 4.1 14.8 - - + -
20B VAL* 3.9 16.9 - - + +
22B ALA* 3.7 24.5 - - + -
27B PHE* 3.7 35.3 - - + +
25C PHE* 4.4 5.4 - - + -
69C ARG 3.6 13.5 - - - +
70C VAL* 1.3 74.6 - - - +
72C GLN* 1.3 60.8 + - + +
99C PRO* 3.8 0.9 - - - -
100C ALA* 2.9 27.7 + - - +
120C VAL* 2.9 26.4 + - + +
121C ALA* 4.5 0.7 - - - -
122C LEU* 3.9 11.4 - - + -
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Residues in contact with GLN 72 (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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72A GLN* 5.0 2.6 + - - -
27B PHE* 3.6 36.6 - - + +
28B VAL 5.7 2.7 + - - +
72B GLN* 5.1 2.6 + - - -
118B ALA* 6.1 2.8 - - - +
119B CYS 4.9 2.6 + - - -
120B VAL* 3.7 17.0 - - - +
70C VAL* 3.6 1.4 - - - +
71C VAL* 1.3 85.4 - - + +
73C THR* 1.3 70.9 + - - +
74C THR* 4.2 12.3 + - - -
100C ALA* 3.2 13.2 - - + +
101C ARG* 5.6 0.4 - - - -
119C CYS* 3.2 7.3 - - - +
120C VAL* 2.9 52.3 + - + +
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Residues in contact with THR 73 (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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70C VAL* 3.6 19.5 - - + -
72C GLN* 1.3 86.2 - - - +
74C THR* 1.3 63.5 + - - +
75C CYS* 3.7 9.3 - - - -
90C TYR* 2.7 29.2 + - + +
94C PHE* 4.1 13.7 - - + -
99C PRO* 4.1 3.4 - - + -
100C ALA 2.9 8.5 + - - -
101C ARG* 3.1 19.1 - - - +
102C ALA* 3.2 21.3 + - - +
117C VAL* 4.3 4.7 - - + -
118C ALA 3.4 7.9 - - - -
119C CYS* 3.9 8.5 - - + +
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Residues in contact with THR 74 (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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74A THR* 6.1 2.5 - - + -
74B THR* 6.0 3.8 - - + -
76B PHE* 5.5 7.2 - - + -
72C GLN* 4.2 14.0 + - - -
73C THR* 1.3 74.4 + - - +
75C CYS* 1.3 63.1 + - - +
76C PHE* 3.5 33.7 - - + -
102C ALA* 3.7 12.6 - - + +
116C GLU 3.9 1.0 - - - +
117C VAL* 3.5 2.4 - - - -
118C ALA* 2.9 41.0 + - - +
119C CYS* 5.6 0.7 - - - -
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Residues in contact with CYS 75 (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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73C THR* 3.7 20.9 - - - -
74C THR* 1.3 79.3 - - - +
76C PHE* 1.3 67.4 + - - +
77C LEU* 5.8 0.2 - - + -
86C PHE* 3.6 34.3 - - + -
90C TYR* 4.0 2.7 - - - -
101C ARG* 3.8 15.7 - - - -
102C ALA 2.9 10.2 + - - +
103C THR* 3.3 16.8 - - + +
104C VAL* 3.1 24.3 + - - +
116C GLU 3.7 3.1 - - - -
117C VAL* 4.0 15.3 - - + -
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Residues in contact with PHE 76 (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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74A THR* 5.0 10.3 - - + -
76A PHE* 4.6 8.3 - + - -
102A ALA* 4.6 16.2 - - + -
104A VAL* 3.6 30.7 - - + -
76B PHE* 4.3 17.7 - + - -
74C THR* 3.5 34.1 - - + -
75C CYS* 1.3 75.6 - - - +
77C LEU* 1.3 65.8 + - - +
104C VAL* 3.5 28.3 - - + +
106C VAL* 4.1 9.6 - - + -
109C LEU* 3.7 20.1 - - + +
115C VAL* 3.3 4.9 - - - +
116C GLU* 2.9 49.1 + - + +
118C ALA* 5.7 1.1 - - + -
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Residues in contact with LEU 77 (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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45C ILE* 4.1 8.3 - - + -
76C PHE* 1.3 82.9 - - - +
78C ALA* 1.3 60.6 + - - +
79C ASP 4.0 11.4 - - - +
82C ASP* 4.2 2.5 - - + -
83C PHE* 3.3 57.7 - - + +
86C PHE* 4.0 22.0 - - + -
103C THR* 4.3 9.9 - - + -
104C VAL 2.9 12.2 + - - +
105C ALA* 3.0 3.6 - - - -
106C VAL* 2.8 28.9 + - - +
109C LEU* 4.1 3.8 - - - -
114C ARG 3.4 13.2 - - - +
115C VAL* 3.8 18.6 - - + -
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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