Contacts of the strand formed by residues 25 - 31 (chain F) 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 PHE 25 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D PHE* 4.0 14.6 - + - -
22E ALA 3.6 19.5 - - - -
23E GLY* 3.7 15.0 - - - -
25E PHE* 3.9 24.2 - + - -
27E PHE* 3.8 27.6 - + - -
21F LYS* 3.4 4.3 - - - +
22F ALA 3.0 31.1 + - - +
23F GLY 3.6 15.7 - - - -
24F GLY* 1.3 80.9 + - - +
26F VAL* 1.3 65.6 + - - +
27F PHE* 3.8 16.6 - + + -
71F VAL* 4.5 3.1 - - + -
120F VAL* 3.8 17.0 - - + -
121F ALA 3.2 17.9 - - - +
122F LEU* 3.8 22.4 - - + -
123F ALA* 4.1 1.8 - - - +
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Residues in contact with VAL 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ALA* 4.1 10.1 - - + -
20F VAL 3.5 6.1 - - - +
21F LYS* 4.1 16.6 - - + -
25F PHE* 1.3 77.8 - - - +
27F PHE* 1.3 63.5 + - - +
28F VAL* 3.7 21.1 + - + +
60F LEU* 4.6 4.3 - - + -
63F ALA* 3.6 29.4 - - + +
65F SER* 4.1 11.0 - - - -
119F CYS 3.9 0.2 - - - +
120F VAL* 3.4 5.4 - - - -
121F ALA* 2.7 38.9 + - + +
123F ALA* 3.8 22.4 - - + -
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Residues in contact with PHE 27 (chain F).
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* 3.8 25.4 - + - -
71D VAL* 3.7 43.1 - - + +
72D GLN* 3.7 30.1 - - + +
100D ALA* 3.2 9.3 - - + +
120D VAL* 4.5 11.9 - - + -
19F ALA* 3.1 3.5 - - - -
20F VAL 2.8 47.0 + - - +
22F ALA* 3.7 23.3 - - + -
25F PHE* 3.8 16.2 - + + -
26F VAL* 1.3 71.9 - - - +
28F VAL* 1.3 61.9 + - - +
119F CYS 3.8 2.9 - - - -
120F VAL* 3.8 21.1 - - + -
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Residues in contact with VAL 28 (chain F).
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* 5.7 2.9 + - - +
100D ALA* 4.2 2.8 - - - +
18F GLN 3.8 9.9 - - - +
19F ALA* 4.2 3.8 - - + -
26F VAL* 3.9 14.8 - - + +
27F PHE* 1.3 75.5 - - - +
29F SER* 1.3 76.0 + - - +
31F GLN* 3.9 6.5 - - - +
56F LEU* 3.9 20.4 - - + +
59F VAL* 3.9 15.7 - - + -
60F LEU* 3.7 21.3 - - + -
118F ALA* 3.4 5.2 - - - +
119F CYS* 2.8 53.1 + - - +
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Residues in contact with SER 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ALA* 3.2 3.2 - - - +
101D ARG 2.8 33.6 + - - +
16F TYR* 3.5 19.9 - - - -
17F ALA 2.6 24.5 + - - -
18F GLN 2.9 16.9 + - - -
28F VAL* 1.3 81.4 - - - +
30F GLY* 1.3 65.9 + - - +
31F GLN* 3.0 18.9 + - - +
117F VAL 3.6 2.9 - - - +
118F ALA* 3.9 0.7 - - - -
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Residues in contact with GLY 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ARG 2.8 14.6 + - - +
102D ALA* 4.5 0.2 - - - -
16F TYR* 4.8 10.2 + - - -
29F SER* 1.3 73.1 - - - +
31F GLN* 1.3 65.1 + - - +
32F ILE* 3.9 5.7 + - - +
116F GLU* 3.6 26.6 - - - +
117F VAL 3.5 10.1 - - - -
118F ALA* 3.6 14.5 - - - +
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Residues in contact with GLN 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ALA* 4.7 0.8 - - - +
10F PRO* 4.6 12.5 + - - +
16F TYR* 5.8 0.7 - - - -
18F GLN* 3.9 12.9 - - - +
28F VAL* 3.9 6.8 - - - +
29F SER* 3.0 21.3 - - - +
30F GLY* 1.3 73.9 - - - +
32F ILE* 1.3 61.1 + - - +
52F VAL* 3.6 25.1 - - + +
55F ASN* 3.5 24.5 - - + +
56F LEU* 3.5 33.7 - - + +
59F VAL* 4.1 19.1 - - - +
116F GLU* 3.2 6.6 - - - -
117F VAL 2.8 33.5 + - - +
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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