Contacts of the strand formed by residues 60 - 68 (chain B) in PDB entry 3CFV
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 TYR 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B LYS* 4.3 4.3 - - - +
55B PRO* 3.7 23.8 - - + +
58B LYS* 3.4 44.3 + - + +
59B ASP* 1.3 92.8 - - - +
61B ALA* 1.3 63.4 - - - +
62B LEU* 3.4 27.8 - - + +
84B HIS* 3.5 46.6 + + + -
85B ILE 3.4 15.5 - - - +
86B PRO* 3.9 8.1 - - + -
87B ASN* 3.3 13.1 + - - +
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B VAL* 4.6 4.0 - - + -
53B THR 3.6 10.3 - - - +
54B LYS* 4.3 20.0 - - + +
55B PRO* 4.3 0.4 - - - -
60B TYR* 1.3 75.2 - - - +
62B LEU* 1.3 65.0 + - - +
63B HIS* 3.6 23.0 + - + -
83B VAL 3.3 4.0 - - - +
84B HIS* 3.4 1.7 - - - -
85B ILE* 2.7 37.8 + - + +
87B ASN* 4.3 6.7 - - - +
385B GLU* 6.2 0.4 - - + +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 3.4 12.3 - - - +
53B THR* 2.9 47.6 + - + -
55B PRO* 4.3 12.8 - - + -
60B TYR* 3.4 17.7 - - + +
61B ALA* 1.3 71.6 - - - +
63B HIS* 1.3 59.7 + - - +
64B TRP* 3.6 26.4 - - + -
82B ARG* 4.3 17.7 - - + -
83B VAL 3.5 1.3 - - - -
84B HIS* 3.3 35.0 - - + +
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Residues in contact with HIS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TRP* 3.6 19.1 - + + -
51B GLU 4.4 3.1 - - - -
52B VAL* 3.5 24.8 - - + +
54B LYS* 6.2 0.4 - - - -
61B ALA* 3.6 29.5 + - + -
62B LEU* 1.3 74.2 - - - +
64B TRP* 1.3 73.8 + - - +
82B ARG* 3.5 1.4 - - - +
83B VAL* 2.8 38.6 + - + -
85B ILE* 3.5 24.8 - - + +
382B ASN* 3.2 28.5 + - - -
383B PRO* 6.0 0.4 - - + -
384B ASN* 4.4 5.4 - - + +
385B GLU* 4.0 21.3 - - + +
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Residues in contact with TRP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B TRP* 3.4 10.7 - - - -
49B LEU* 2.9 50.3 + - + +
51B GLU* 3.4 38.0 + - + -
52B VAL* 4.3 3.8 - - - -
53B THR* 4.3 11.2 - - + -
62B LEU* 3.6 36.3 - - + -
63B HIS* 1.3 76.6 - - - +
65B LEU* 1.3 64.7 + - - +
80B VAL* 4.1 13.5 - - + -
81B ALA 3.2 15.5 - - - +
82B ARG* 3.5 27.4 - - + +
117B GLU* 2.6 31.4 + - + -
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 5.0 2.7 - - + -
47B GLN 3.6 7.6 - - - +
48B TRP* 3.2 66.0 - - + +
64B TRP* 1.3 74.3 - - - +
66B VAL* 1.3 62.9 + - - +
67B LEU* 3.9 14.5 + - + -
80B VAL* 3.1 8.3 - - - +
81B ALA* 2.8 37.6 + - + +
83B VAL* 3.7 26.7 - - + -
390B CYS* 4.4 7.9 - - + -
398B MSE 4.0 19.1 - - + -
400B ILE* 4.1 8.1 - - + -
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B THR* 3.9 2.6 + - - +
46B VAL* 3.4 9.0 + - - +
47B GLN* 2.7 46.9 + - + +
49B LEU* 3.4 37.0 - - + -
65B LEU* 1.3 73.6 - - - +
67B LEU* 1.3 62.6 + - - +
78B LEU* 4.1 13.5 - - + -
79B VAL 3.5 4.7 - - - +
80B VAL* 4.5 3.1 - - + +
129B ALA* 3.9 28.4 - - + +
130B ARG 5.2 0.2 - - - +
131B TYR* 5.0 2.5 - - + -
139B ILE* 4.2 22.4 - - + -
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 4.3 16.4 - - + -
43B SER* 3.7 18.4 - - - +
45B THR* 3.9 8.3 - - - -
46B VAL* 3.3 33.7 - - + -
65B LEU* 4.3 5.2 - - + -
66B VAL* 1.3 76.3 - - - +
68B GLY* 1.3 61.7 + - - +
78B LEU* 3.5 14.0 - - - +
79B VAL* 2.6 46.6 + - + +
81B ALA* 3.8 28.5 - - + -
114B ILE* 4.8 0.7 - - + -
392B VAL* 4.2 2.5 - - + -
398B MSE 3.7 29.2 - - + -
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 5.6 0.7 - - - +
41B TRP 4.9 2.1 - - - +
42B PRO 4.0 0.7 - - - +
43B SER* 3.1 31.3 + - - -
44B LEU 5.3 0.9 - - - -
45B THR* 3.9 5.0 - - - +
67B LEU* 1.3 77.1 - - - +
69B THR* 1.3 64.4 + - - -
77B HIS 3.6 10.1 - - - -
79B VAL* 4.4 3.8 - - - +
126B VAL* 3.9 19.1 - - - -
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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