Contacts of the strand formed by residues 60 - 67 (chain B) in PDB entry 1FZV
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 CYS 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A SER* 2.8 34.7 + - - -
68A GLY* 4.1 5.2 - - - -
69A CYS* 2.1 55.9 - - + -
41B LEU* 4.4 8.7 - - - -
42B VAL 3.1 21.1 - - - +
43B ASP* 4.4 2.7 - - - +
44B VAL 4.2 0.7 - - - +
58B PRO* 3.2 6.8 - - - +
59B SER* 1.3 81.2 + - - +
61B VAL* 1.3 66.6 + - - +
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Residues in contact with VAL 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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29A VAL* 4.0 10.1 - - + -
33A SER* 4.0 6.3 - - - -
40B ARG 3.5 0.5 - - - +
41B LEU* 3.2 3.1 - - - -
42B VAL* 2.7 57.3 + - + +
44B VAL* 3.7 17.9 - - + -
58B PRO* 4.8 0.4 - - + -
60B CYS* 1.3 79.7 - - - +
62B SER* 1.3 59.2 + - - +
63B LEU* 3.6 14.5 + - + -
87B MET* 3.8 24.7 - - - -
89B LEU* 3.9 15.7 - - + -
105B PHE* 4.0 22.4 - - + -
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Residues in contact with SER 62 (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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29A VAL 5.7 0.4 + - - -
32A ARG* 3.4 30.3 + - - +
33A SER* 4.2 2.0 - - - -
39B GLU* 2.5 32.8 + - - +
40B ARG 3.4 5.6 - - - -
41B LEU* 3.6 16.1 - - - +
61B VAL* 1.3 74.2 - - - +
63B LEU* 1.3 58.1 + - - +
87B MET* 3.5 20.3 - - - +
107B GLN* 4.9 2.8 + - - -
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Residues in contact with LEU 63 (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 GLU* 4.3 2.5 - - - -
40B ARG* 2.8 36.3 + - - +
42B VAL* 3.5 27.8 - - + -
47B GLU* 3.8 7.2 - - - +
61B VAL* 3.6 8.5 + - + -
62B SER* 1.3 73.5 - - - +
64B LEU* 1.3 63.7 + - - +
65B ARG* 3.3 35.9 + - - +
85B VAL* 3.7 9.9 - - + -
87B MET* 3.5 30.5 - - + -
105B PHE* 3.5 28.3 - - + -
106B SER 3.8 2.7 - - - +
107B GLN* 3.4 7.9 - - - +
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Residues in contact with LEU 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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37B ALA* 4.3 14.8 - - + +
38B LEU 3.8 3.4 - - - -
39B GLU* 3.6 29.2 - - + +
63B LEU* 1.3 71.6 - - - +
65B ARG* 1.3 81.3 + - - +
107B GLN* 2.7 33.0 + - + +
108B HIS* 3.1 33.6 + - - +
109B VAL* 5.1 5.8 - - + +
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Residues in contact with ARG 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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37B ALA* 4.3 0.4 - - - -
38B LEU 2.9 31.8 + - - +
40B ARG* 4.3 26.0 - - + +
42B VAL* 4.5 7.7 - - + +
47B GLU* 2.9 34.6 + - - -
63B LEU* 3.3 19.9 + - - +
64B LEU* 1.3 102.3 + - - +
66B CYS* 1.3 66.1 + - - +
67B THR* 3.0 13.8 + - - +
106B SER* 2.8 43.8 + - - +
108B HIS* 3.6 29.0 + - - -
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Residues in contact with CYS 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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36B ARG 3.4 0.4 - - - -
65B ARG* 1.3 71.9 - - - +
67B THR* 1.3 63.3 + - - +
77B CYS* 3.9 17.0 - - - +
78B VAL 4.1 6.5 - - - -
79B PRO* 3.3 35.9 - - + -
108B HIS* 3.0 21.1 + - + +
110B ARG 3.9 0.4 - - - -
111B CYS* 2.0 53.6 - - + -
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Residues in contact with THR 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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41A LEU* 3.5 36.2 - - + +
36B ARG* 2.8 32.0 + - - +
38B LEU* 4.4 13.9 + - + +
40B ARG* 3.7 27.6 + - - +
65B ARG* 3.0 14.0 + - - +
66B CYS* 1.3 78.2 + - - +
68B GLY* 1.3 61.4 + - - +
77B CYS* 3.7 8.0 - - - -
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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