Contacts of the strand formed by residues 53 - 58 (chain B) in PDB entry 3FJC
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 GLU 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ALA* 3.2 20.1 - - - +
49B GLU* 3.2 14.2 + - - +
50B SER* 3.0 43.8 + - - +
51B VAL 4.3 3.4 - - - +
52B GLY* 1.3 78.7 - - - +
54B VAL* 1.3 68.7 + - - +
84B LEU* 4.1 11.6 - - + +
85B PHE 3.3 7.4 - - - +
86B LEU* 4.1 15.6 - - + +
88B ARG* 6.0 0.4 - - - +
100B LYS* 2.7 43.7 + - + +
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B TYR* 3.1 42.0 - - + +
46B LEU* 4.0 17.5 - - + -
47B SER 3.1 10.5 - - - +
48B ALA* 4.4 0.2 - - - +
49B GLU 4.7 0.7 - - - +
53B GLU* 1.3 81.8 - - - +
55B TYR* 1.3 66.3 + - - +
56B ILE* 4.1 11.7 - - + -
83B CYS 3.5 4.5 - - - +
84B LEU* 3.6 6.5 - - - +
85B PHE* 2.9 40.3 + - + +
87B GLU* 4.0 12.1 - - + +
97B TYR* 4.1 15.3 - - + -
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Residues in contact with TYR 55 (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 GLN 3.9 0.6 - - - +
46B LEU* 3.2 26.7 - - - +
47B SER* 2.9 28.2 + - - +
48B ALA 5.4 0.2 - - - -
49B GLU* 3.3 33.6 + - + -
54B VAL* 1.3 74.5 - - - +
56B ILE* 1.3 61.8 + - - +
57B LYS 3.9 0.7 - - - -
64B TYR* 4.0 18.6 - + + -
79B PRO* 3.8 32.3 + - + -
80B ASN 4.0 14.5 + - - -
83B CYS* 3.7 21.5 - - + -
84B LEU* 3.7 36.6 - - + +
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Residues in contact with ILE 56 (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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14B LEU* 3.9 20.2 - - + -
44B TRP* 3.4 35.0 - - + -
45B GLN 4.1 1.8 - - - -
46B LEU* 4.0 13.7 - - + -
54B VAL* 4.1 7.6 - - + -
55B TYR* 1.3 78.5 - - - +
57B LYS* 1.3 56.7 + - - +
64B TYR* 3.6 3.1 - - - -
65B LEU* 2.8 50.3 + - + +
83B CYS 4.6 4.2 + - - -
85B PHE* 4.0 21.3 - - + -
97B TYR* 3.9 33.2 - - + -
109B VAL* 5.3 0.7 - - + -
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Residues in contact with LYS 57 (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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44B TRP* 3.4 6.8 - - - -
45B GLN* 2.7 55.9 + - - +
55B TYR* 3.9 0.4 - - + -
56B ILE* 1.3 72.4 - - - +
58B SER* 1.3 75.8 + - - +
59B THR* 5.5 3.4 - - - +
62B GLY* 3.3 26.0 - - - +
63B GLN 3.3 13.7 - - - +
64B TYR* 3.5 39.7 + - + +
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Residues in contact with SER 58 (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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25B ILE* 3.7 27.1 + - - +
41B HIS* 4.9 6.6 - - - -
43B GLN 3.7 10.1 + - - -
44B TRP* 3.5 8.6 - - - -
57B LYS* 1.3 74.5 - - - +
59B THR* 1.3 59.6 + - - +
60B GLU* 3.2 12.4 + - - +
61B THR* 3.4 26.3 + - - +
62B GLY* 2.8 29.1 + - - -
63B GLN 2.7 14.5 + - - -
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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