Contacts of the strand formed by residues 33 - 38 (chain B) in PDB entry 3F7V
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 ILE 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.2 7.2 - - + -
23B CYS* 4.0 18.6 - - - -
25B ALA* 5.7 0.2 - - + -
29B ILE* 3.5 23.6 - - + -
31B THR 2.8 6.1 + - - -
32B ASP* 1.3 72.5 - - - +
34B HIS* 1.3 69.1 + - - +
35B TRP* 4.5 7.0 - - - +
51B ALA* 2.8 40.1 + - + -
71B PHE* 3.1 52.7 - - + -
88B CYS* 4.2 14.6 - - + -
89B GLN 3.5 8.3 - - - +
90B GLN* 3.6 14.6 - - + -
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Residues in contact with HIS 34 (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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103A GLY 3.7 7.9 + - - -
104A TYR* 3.6 24.5 - + + -
32B ASP 4.2 3.7 + - - -
33B ILE* 1.3 79.4 + - - +
35B TRP* 1.3 67.3 + - - +
36B TYR* 3.8 11.0 - - + +
46B LEU* 4.4 1.6 - - + -
48B ILE 3.6 8.7 - - - +
49B LYS* 3.7 3.6 - - - +
50B TYR* 2.8 51.3 + + - -
87B TYR 3.8 0.2 - - - +
88B CYS* 3.2 5.3 - - - -
89B GLN* 2.7 75.7 + - - +
91B SER* 3.0 24.4 + - - -
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Residues in contact with TRP 35 (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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6B GLN* 3.9 21.3 - - - -
21B PHE* 3.8 22.7 - - + -
23B CYS* 3.9 29.4 - - + -
33B ILE* 4.5 16.8 - - + +
34B HIS* 1.3 77.7 - - - +
36B TYR* 1.3 61.2 + - - +
46B LEU* 3.6 5.4 - - - +
47B LEU* 2.7 30.6 + - + -
48B ILE* 2.8 40.2 + - + +
51B ALA 4.9 5.0 + - - -
64B GLY* 5.5 0.4 - - - -
65B SER 5.7 0.4 + - - -
71B PHE* 4.2 8.2 - - + +
72B THR 4.0 7.1 + - - -
73B LEU* 3.3 64.3 - - + +
86B TYR* 4.6 4.0 - - + -
87B TYR 3.4 21.8 - - - -
88B CYS* 4.1 7.9 - - + -
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Residues in contact with TYR 36 (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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45A LEU* 5.5 0.9 - - + -
104A TYR* 3.6 5.0 - - - +
105A PHE* 2.8 49.9 + + - -
108A TRP* 3.5 24.2 - + - -
34B HIS* 3.8 14.4 - - + -
35B TRP* 1.3 74.2 - - - +
37B GLN* 1.3 61.9 + - - +
44B PRO* 4.3 12.6 - - + -
45B ARG 3.2 5.2 - - - +
46B LEU* 3.5 27.8 - - + -
47B LEU* 3.9 6.7 - - - +
85B ASN 3.8 0.7 - - - +
86B TYR* 3.5 6.2 - - - +
87B TYR* 3.0 45.7 + - + +
89B GLN* 2.5 46.1 + - + -
98B PHE* 4.3 8.3 - + - -
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Residues in contact with GLN 37 (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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36B TYR* 1.3 74.6 - - - +
38B GLN* 1.3 63.8 + - - +
39B ARG* 3.2 42.0 + - - +
43B SER 3.6 0.9 - - - +
44B PRO* 3.3 2.9 - - - +
45B ARG* 2.6 56.8 + - + +
47B LEU* 3.6 24.8 - - + +
62B PHE* 4.1 14.8 - - - -
81B GLU 4.3 4.9 + - - -
82B ASP* 4.4 2.0 + - - -
84B ALA* 3.8 19.1 - - + +
85B ASN 3.8 2.0 - - - -
86B TYR* 3.3 26.8 + - + -
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Residues in contact with GLN 38 (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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39A GLN* 3.0 40.5 + - - -
45A LEU* 4.1 0.3 - - - +
95A TYR* 3.2 8.3 + - - -
37B GLN* 1.3 76.9 - - - +
39B ARG* 1.3 66.8 + - - +
40B THR 4.0 0.2 + - - -
41B ASN 5.7 0.4 - - - +
42B GLY 3.1 28.0 + - - +
43B SER 4.1 4.0 - - - -
44B PRO* 3.7 27.3 - - + +
84B ALA* 3.8 3.4 - - - -
85B ASN* 3.0 44.2 + - + +
87B TYR* 3.8 19.6 + - + -
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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