Contacts of the strand formed by residues 100 - 105 (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 ALA 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D VAL 2.9 17.6 + - - +
72D GLN* 3.3 6.5 - - + -
73D THR 3.0 23.7 + - - -
99D PRO* 1.3 77.1 - - - +
101D ARG* 1.3 60.5 + - - +
17F ALA 3.8 5.8 - - - +
20F VAL* 3.7 7.3 - - + +
27F PHE* 3.2 36.3 - - + +
28F VAL 4.2 1.1 - - - -
29F SER* 3.2 16.6 - - - +
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Residues in contact with ARG 101 (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* 5.5 0.9 - - - -
73D THR* 3.1 19.5 - - - +
75D CYS* 3.8 11.2 - - - -
86D PHE* 3.6 16.0 - - - -
87D ASN* 2.8 35.7 + - - +
90D TYR* 3.6 26.2 - - - +
99D PRO 3.8 0.2 + - - -
100D ALA* 1.3 76.9 - - - +
102D ALA* 1.3 63.5 + - - +
103D THR* 3.1 27.0 + - - +
14F GLY* 4.1 3.2 - - - -
15F PRO* 3.5 20.8 - - - +
16F TYR* 3.6 44.2 - - + -
29F SER* 2.8 17.9 + - - +
30F GLY* 2.8 23.3 + - - +
118F ALA* 5.7 0.2 - - - -
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Residues in contact with ALA 102 (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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73D THR 3.2 8.2 + - - +
74D THR* 3.7 11.3 - - + +
75D CYS* 2.8 27.6 + - - +
101D ARG* 1.3 76.0 - - - +
103D THR* 1.3 64.8 + - - +
104D VAL* 5.3 0.4 - - - -
30F GLY 4.2 0.2 - - - +
74F THR* 5.9 1.3 - - + -
76F PHE* 4.5 16.2 - - + -
116F GLU* 3.4 12.6 - - - +
118F ALA* 4.2 22.2 - - + -
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Residues in contact with THR 103 (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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75D CYS* 3.3 19.2 - - + +
77D LEU* 4.7 5.6 - - + -
83D PHE* 3.6 32.1 - - + -
86D PHE* 4.9 5.6 - - + -
101D ARG* 3.1 36.4 + - - +
102D ALA* 1.3 76.3 + - - +
104D VAL* 1.3 66.5 + - - +
110F PRO* 3.4 18.1 - - - +
116F GLU* 2.6 31.8 + - - +
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Residues in contact with VAL 104 (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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75D CYS 3.1 4.5 + - - +
76D PHE* 3.5 34.3 - - + -
77D LEU* 2.9 25.1 + - - +
83D PHE* 4.3 8.5 - - - -
102D ALA 5.3 0.2 - - - -
103D THR* 1.3 82.4 - - - +
105D ALA* 1.3 61.7 + - - +
106D VAL* 3.8 11.9 - - + -
76F PHE* 3.6 35.0 - - + -
106F VAL* 4.1 9.4 - - + -
108F ALA 3.8 4.9 - - - +
109F LEU* 3.6 23.3 - - + +
116F GLU* 3.8 1.6 - - - +
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Residues in contact with ALA 105 (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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77D LEU* 3.1 9.6 - - - +
79D ASP* 4.0 5.2 - - - -
80D MSE 3.6 32.1 - - + +
83D PHE* 4.3 3.1 - - + -
104D VAL* 1.3 74.1 - - - +
106D VAL* 1.3 60.3 + - - +
106F VAL* 3.4 5.4 - - - +
107F LYS* 3.1 24.9 + - - -
108F ALA* 2.8 32.7 + - + +
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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