Contacts of the strand formed by residues 53 - 57 (chain S) 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 GLU 53 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49S ILE* 3.4 12.5 - - + +
50S GLN* 2.7 56.0 + - + +
51S ALA 2.9 2.1 + - - +
52S GLU* 1.3 79.7 - - - +
54S LEU* 1.3 75.6 + - - +
55S VAL* 4.4 2.1 - - - +
64S MET* 4.3 0.4 - - - -
65S ALA* 3.1 26.2 + - - +
92S ARG* 3.0 29.3 + - - +
93S THR 3.7 1.9 + - - -
94S GLY* 3.0 23.6 + - - -
95S ASN 3.4 23.1 - - - +
96S ILE* 4.2 2.9 - - - +
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Residues in contact with LEU 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53S GLU* 1.3 86.0 - - - +
55S VAL* 1.3 68.5 + - - +
62S LYS* 5.1 15.3 - - + -
63S GLY 3.3 17.3 - - - +
64S MET* 4.1 5.2 - - + -
78S PHE* 4.6 9.6 - - + -
93S THR* 3.2 31.8 + - + +
95S ASN* 2.9 16.4 + - + +
97S VAL* 3.1 50.0 - - + +
98S ASP* 5.5 4.9 - - - +
113S LEU* 4.9 16.8 - - + -
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Residues in contact with VAL 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46S LEU* 4.4 2.9 - - + -
49S ILE* 3.5 27.1 - - + -
53S GLU 4.4 1.8 - - - +
54S LEU* 1.3 82.1 - - - +
56S GLU* 1.3 61.0 + - - +
57S PHE* 4.1 11.9 - - + -
62S LYS* 3.3 7.1 - - - +
63S GLY 3.0 32.2 + - - +
64S MET* 4.3 0.9 - - - +
75S ILE* 3.5 44.4 - - + -
90S VAL* 4.0 11.0 - - + -
91S LYS 3.6 13.9 - - - +
92S ARG* 4.9 3.1 - - - -
93S THR* 4.2 6.1 - - - -
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Residues in contact with GLU 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55S VAL* 1.3 77.7 - - - +
57S PHE* 1.3 73.0 + - - +
60S GLY* 3.7 29.5 - - - +
61S VAL 3.5 3.6 - - - +
62S LYS* 3.6 20.9 - - + +
90S VAL* 3.7 3.0 - - - +
91S LYS* 3.1 38.1 + - + +
93S THR* 4.4 10.7 - - + +
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Residues in contact with PHE 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33S VAL* 4.1 11.2 - - + -
41S ALA* 4.1 11.0 - - + -
43S VAL* 4.0 13.0 - - + -
55S VAL* 4.1 18.8 - - + -
56S GLU* 1.3 82.1 - - - +
58S SER* 1.3 61.9 + - - +
59S SER* 3.2 3.6 - - - +
60S GLY* 2.9 20.7 + - - -
61S VAL* 2.8 43.0 + - + -
62S LYS* 4.8 0.2 - - - -
63S GLY 4.6 6.3 - - - -
75S ILE* 4.3 14.1 - - + -
77S LEU* 3.6 29.4 - - + -
84S VAL* 4.0 15.7 - - + -
88S GLU* 5.4 2.7 - - + -
89S LEU 3.9 4.3 - - - -
90S VAL* 3.5 31.2 - - + -
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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