Contacts of the strand formed by residues 100 - 105 (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 ALA 100 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E ALA 3.8 5.6 - - - +
20E VAL* 3.7 6.4 - - - +
27E PHE* 3.2 36.1 - - + +
28E VAL 4.2 1.1 - - - -
29E SER* 3.2 17.9 - - - +
71F VAL 2.9 18.0 + - - +
72F GLN* 3.4 5.8 - - + -
73F THR* 3.0 24.4 + - - -
99F PRO* 1.3 77.6 - - - +
101F ARG* 1.3 61.0 + - - +
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Residues in contact with ARG 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E GLY* 3.7 5.1 - - - -
15E PRO* 3.3 26.4 - - - +
16E TYR* 3.5 45.4 - - + -
29E SER* 2.8 18.0 + - - +
30E GLY* 2.9 22.6 + - - +
72F GLN* 5.6 0.4 - - - -
73F THR* 3.1 18.6 - - - +
75F CYS* 3.8 9.6 - - - -
83F PHE* 6.2 0.8 - - - -
86F PHE* 3.7 9.9 - - - -
87F ASN* 2.8 31.4 + - - +
90F TYR* 3.5 32.4 - - - +
99F PRO 3.8 0.2 + - - -
100F ALA* 1.3 76.9 - - - +
102F ALA* 1.3 64.1 + - - +
103F THR* 3.2 24.9 + - - +
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Residues in contact with ALA 102 (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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74E THR* 6.1 0.9 - - + -
76E PHE* 4.9 12.8 - - + -
116E GLU* 3.7 14.6 - - - +
118E ALA* 4.1 22.7 - - + -
73F THR 3.3 7.7 + - - +
74F THR* 3.7 10.7 - - + +
75F CYS* 2.8 27.6 + - - +
101F ARG* 1.3 76.9 - - - +
103F THR* 1.3 61.8 + - - +
104F VAL* 5.3 0.9 - - - -
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Residues in contact with THR 103 (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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110E PRO* 3.5 13.8 - - - +
116E GLU* 3.0 24.1 + - - +
75F CYS* 3.2 21.5 - - + +
77F LEU* 4.2 16.4 - - + -
83F PHE* 3.7 26.7 - - + -
86F PHE* 4.3 8.1 - - + -
87F ASN* 5.8 0.2 - - - +
101F ARG* 3.2 35.8 + - - +
102F ALA* 1.3 75.8 + - - +
104F VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 104 (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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76E PHE* 3.8 33.7 - - + -
106E VAL* 4.4 4.5 - - + -
108E ALA 3.9 7.6 - - - +
109E LEU* 3.5 23.6 - - + -
116E GLU* 3.6 7.4 - - - +
75F CYS 3.1 4.3 + - - +
76F PHE* 3.4 33.7 - - + -
77F LEU* 2.9 24.1 + - - +
83F PHE* 4.2 8.5 - - - -
102F ALA 5.3 0.4 - - - -
103F THR* 1.3 83.5 - - - +
105F ALA* 1.3 59.7 + - - +
106F VAL* 3.9 9.8 + - + -
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Residues in contact with ALA 105 (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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106E VAL* 3.4 5.7 - - - +
107E LYS* 3.1 24.8 + - + -
108E ALA* 2.9 36.5 + - + +
77F LEU* 3.1 12.1 - - - +
78F ALA 4.8 0.9 - - - -
79F ASP* 4.3 3.6 - - - +
80F MSE 3.9 20.9 - - - +
83F PHE* 4.1 11.1 - - + -
104F VAL* 1.3 73.0 - - - +
106F VAL* 1.3 59.9 + - - +
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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