Contacts of the strand formed by residues 31 - 37 (chain J) in PDB entry 3FKS
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 GLY 31 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27J LEU* 6.0 0.9 - - - -
30J THR* 1.3 76.9 - - - +
32J ARG* 1.3 64.2 - - - +
43J VAL* 3.7 6.5 - - - -
44J PHE 3.2 13.0 - - - -
45J GLY* 4.2 0.2 - - - -
46J LEU* 3.8 13.5 - - - -
88J GLU 3.2 0.5 - - - +
89J LEU* 3.6 2.9 - - - +
90J VAL* 2.6 42.5 + - - +
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Residues in contact with ARG 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J LEU* 6.2 2.9 - - + +
30J THR* 6.4 0.4 - - - -
31J GLY* 1.3 78.4 - - - -
33J VAL* 1.3 64.0 - - - +
34J LEU 3.3 0.3 + - - -
43J VAL* 3.5 3.6 - - - -
44J PHE* 2.8 42.3 + - + +
87J GLY* 3.5 26.2 + - - -
88J GLU 3.2 12.3 - - - -
89J LEU* 3.9 35.2 - - + +
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Residues in contact with VAL 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J ARG* 1.3 70.3 - - - +
34J LEU* 1.3 62.6 + - - +
35J ALA 3.7 26.2 - - - +
36J VAL* 4.2 9.9 - - + -
41J ALA* 5.3 1.1 - - + -
42J ARG 4.1 4.9 - - - +
43J VAL* 4.2 6.7 - - + +
57J PHE* 4.1 7.2 - - + -
84J VAL* 3.9 12.3 - - + -
85J LYS 3.7 11.4 - - - +
86J GLU* 4.0 6.9 - - - +
87J GLY* 2.8 27.2 + - - +
88J GLU* 3.1 40.3 + - + +
90J VAL* 3.9 14.1 - - + -
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Residues in contact with LEU 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J ARG 3.3 3.1 + - - +
33J VAL* 1.3 74.5 - - - +
35J ALA* 1.3 68.3 + - + +
42J ARG* 2.8 39.6 + - + +
44J PHE* 4.4 27.6 - - + +
71J GLY 5.6 0.4 - - - +
72J GLN* 4.8 18.4 - - + +
86J GLU* 3.7 10.6 - - - +
54M LEU 5.1 3.4 - - - +
55M GLY* 3.4 18.1 - - - -
56M GLU* 4.5 5.3 + - + +
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Residues in contact with ALA 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J VAL* 3.6 6.4 - - - +
34J LEU* 1.3 84.2 - - + +
36J VAL* 1.3 63.6 + - - +
42J ARG* 2.9 55.1 + - + +
86J GLU* 5.2 0.9 - - - -
53M HIS* 3.3 18.4 - - - +
54M LEU* 3.3 16.6 - - - +
55M GLY* 4.7 0.2 - - - -
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Residues in contact with VAL 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J VAL* 4.2 2.9 - - + -
35J ALA* 1.3 75.0 - - - +
37J GLY* 1.3 67.5 + - - +
40J ILE 3.2 15.3 - - - +
41J ALA* 4.1 7.9 - - + -
77J LEU* 4.3 8.7 - - + -
81J ASP* 4.5 3.8 - - + +
84J VAL* 3.3 54.7 - - + +
85J LYS* 4.6 4.3 - - - -
86J GLU 4.8 0.2 - - - +
33M ILE* 4.2 3.4 - - + -
52M GLN* 3.4 3.5 - - - +
53M HIS* 2.9 57.8 + - + +
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Residues in contact with GLY 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36J VAL* 1.3 79.1 - - - +
38J ASP* 1.3 70.4 + - - +
39J GLY 3.2 3.1 - - - -
40J ILE* 2.9 29.0 + - - +
81J ASP* 4.6 2.0 - - - -
33M ILE* 3.9 13.7 - - - -
52M GLN* 3.8 15.3 - - - -
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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