Contacts of the strand formed by residues 70 - 77 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D LEU* 3.5 31.4 - - + -
66D GLY 3.7 2.2 - - - +
67D LEU 3.1 18.2 + - - +
68D SER 3.4 0.4 - - - +
69D ARG* 1.3 75.1 - - - +
71D VAL* 1.3 61.9 + - - +
72D GLN 3.7 4.5 - - - +
73D THR* 3.6 31.2 - - + -
94D PHE* 3.7 15.3 - - + -
99D PRO* 3.4 16.3 - - + +
119D CYS* 4.0 8.5 - - + -
120D VAL 3.6 9.2 - - - +
121D ALA* 3.7 11.0 - - + -
1F MSE 3.0 18.5 - - - +
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Residues in contact with VAL 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PHE* 4.4 5.2 - - + -
69D ARG 3.4 11.2 + - - +
70D VAL* 1.3 77.0 - - - +
72D GLN* 1.3 62.8 + - + +
99D PRO* 3.8 1.2 - - - +
100D ALA* 2.9 28.2 + - - +
120D VAL* 2.9 25.3 + - + +
121D ALA* 4.5 0.7 - - - -
122D LEU* 4.0 11.9 - - + -
1F MSE 4.0 16.2 - - - -
20F VAL* 3.9 14.3 - - + +
22F ALA* 3.6 25.6 - - + -
27F PHE* 3.7 35.1 - - + +
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Residues in contact with GLN 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D VAL* 3.7 1.6 - - - +
71D VAL* 1.3 84.3 - - + +
73D THR* 1.3 71.6 + - - +
74D THR* 4.3 11.8 + - - -
100D ALA* 3.3 13.7 - - + +
101D ARG* 5.5 0.4 - - - -
119D CYS* 3.2 6.8 - - - +
120D VAL* 2.8 55.9 + - + +
72E GLN* 5.1 2.1 + - - -
27F PHE* 3.7 35.5 - - + +
28F VAL 5.7 2.7 + - - +
72F GLN* 5.0 3.2 + - - -
118F ALA* 6.1 3.0 - - - +
119F CYS 5.0 3.2 + - - +
120F VAL* 3.8 15.6 - - - +
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Residues in contact with THR 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU* 5.7 0.2 - - + -
70D VAL* 3.6 20.2 - - + -
72D GLN* 1.3 83.4 - - - +
74D THR* 1.3 65.5 + - - +
75D CYS* 3.7 8.5 - - - -
90D TYR* 2.7 31.1 + - + +
94D PHE* 4.3 10.5 - - + -
99D PRO* 4.1 3.4 - - + -
100D ALA 3.0 7.3 + - - -
101D ARG* 3.1 20.1 - - - +
102D ALA* 3.2 21.7 + - - +
117D VAL* 4.2 6.1 - - + -
118D ALA 3.3 7.9 - - - -
119D CYS* 3.8 8.3 - - + +
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Residues in contact with THR 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D GLN* 4.3 13.9 + - - -
73D THR* 1.3 74.4 + - - +
75D CYS* 1.3 62.9 + - - +
76D PHE* 3.5 33.7 - - + -
102D ALA* 3.7 16.1 - - + +
116D GLU 3.9 1.0 - - - +
117D VAL* 3.4 3.3 - - - -
118D ALA* 2.9 39.2 + - - -
119D CYS* 5.7 0.3 - - - -
74E THR* 6.2 2.7 - - + -
74F THR* 6.0 2.7 - - + -
76F PHE* 5.1 9.6 - - + -
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Residues in contact with CYS 75 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D THR* 3.7 21.5 - - - -
74D THR* 1.3 78.3 - - - +
76D PHE* 1.3 64.5 + - - +
77D LEU* 4.3 0.7 - - + -
86D PHE* 3.5 36.1 - - + -
90D TYR* 4.0 2.2 - - - -
101D ARG* 3.8 15.5 - - - -
102D ALA 2.8 12.8 + - - +
103D THR* 3.3 13.2 - - + +
104D VAL* 3.1 27.0 + - - +
116D GLU 3.6 3.4 - - - -
117D VAL* 3.9 14.1 - - + -
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Residues in contact with PHE 76 (chain D).
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* 3.5 37.5 - - + -
75D CYS* 1.3 74.1 - - - +
77D LEU* 1.3 65.2 + - - +
104D VAL* 3.5 28.9 - - + +
106D VAL* 3.9 12.3 - - + -
109D LEU* 3.6 20.5 - - + +
115D VAL* 3.3 4.7 - - - +
116D GLU* 2.8 49.6 + - + +
118D ALA* 5.4 2.0 - - + -
74E THR* 5.5 4.5 - - + -
76E PHE* 4.3 23.8 - + - -
102E ALA* 4.9 15.3 - - + -
104E VAL* 3.8 30.5 - - + -
76F PHE* 4.7 7.0 - + - -
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ILE* 4.0 9.6 - - + -
75D CYS 5.5 0.2 - - - -
76D PHE* 1.3 77.7 - - - +
78D ALA* 1.3 60.2 + - - +
79D ASP 3.9 11.7 - - - +
82D ASP* 3.6 22.9 - - + +
83D PHE* 3.1 36.1 - - + -
86D PHE* 3.8 25.4 - - + -
103D THR* 4.7 3.8 - - + -
104D VAL 2.9 12.5 + - - +
105D ALA* 3.1 5.0 - - - -
106D VAL* 2.8 26.2 + - - +
109D LEU* 4.2 4.0 - - - -
114D ARG 3.3 15.5 - - - +
115D VAL* 3.5 24.5 - - + -
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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