Contacts of the strand formed by residues 72 - 77 (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 GLN 72 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34S LEU* 4.3 18.2 - - + +
42S ARG* 3.1 59.8 + - + +
43S VAL 3.5 15.5 - - - +
44S PHE* 4.3 8.2 - - + +
69S GLU* 3.0 60.2 + - + +
71S GLY* 1.3 73.9 - - - +
73S VAL* 1.3 66.2 + - - +
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Residues in contact with VAL 73 (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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41S ALA 3.3 0.5 - - - +
42S ARG* 4.4 1.1 - - - -
43S VAL* 2.6 40.2 + - + +
45S GLY 4.0 6.3 - - - +
46S LEU* 4.8 10.8 - - + -
49S ILE* 4.9 2.7 - - + -
65S ALA* 3.8 13.9 - - + -
67S ASN 3.6 11.9 - - - +
68S LEU* 3.9 11.9 - - + -
72S GLN* 1.3 83.1 - - - +
74S GLY* 1.3 63.3 + - - +
75S ILE* 3.2 28.4 + - + +
72W ARG* 3.4 33.0 - - - +
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Residues in contact with GLY 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40S ILE* 4.9 3.4 - - - -
41S ALA 3.9 3.6 - - - -
42S ARG* 4.6 9.0 - - - -
65S ALA* 3.7 1.7 - - - -
66S LEU* 3.4 9.0 + - - +
67S ASN* 3.0 44.0 + - - +
69S GLU* 4.4 10.1 + - - -
72S GLN* 4.2 1.2 - - - +
73S VAL* 1.3 68.7 - - - +
75S ILE* 1.3 60.4 + - - -
76S VAL* 5.5 0.3 - - - +
287S LEU* 4.7 14.0 - - - +
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Residues in contact with ILE 75 (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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40S ILE* 3.4 3.8 - - - +
41S ALA* 2.8 44.2 + - - +
43S VAL* 4.3 13.5 - - + -
46S LEU* 4.1 19.1 - - + -
55S VAL* 3.5 42.4 - - + -
57S PHE* 4.3 13.5 - - + -
63S GLY* 4.3 0.7 - - - -
64S MET 3.2 27.6 - - - +
65S ALA* 3.6 14.8 - - + -
73S VAL* 3.5 16.6 - - + +
74S GLY* 1.3 75.5 - - - -
76S VAL* 1.3 65.3 + - - +
77S LEU* 4.0 0.5 + - - +
90S VAL* 4.9 0.9 - - + -
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Residues in contact with VAL 76 (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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39S GLY 3.7 5.2 - - - +
40S ILE* 4.0 16.2 - - + -
63S GLY* 3.2 4.0 - - - -
64S MET* 3.0 54.4 + - + +
66S LEU* 4.0 13.9 - - + -
74S GLY 4.3 0.2 + - - -
75S ILE* 1.3 76.5 - - - +
77S LEU* 1.3 62.5 + - - +
78S PHE* 5.0 0.2 - - - -
243S PRO* 3.8 22.9 - - + -
283S LEU* 4.0 15.0 - - + -
287S LEU* 3.8 31.0 - - + -
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Residues in contact with LEU 77 (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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36S VAL* 4.5 8.5 - - + -
39S GLY* 3.2 29.9 + - - +
40S ILE* 4.1 3.6 - - - +
41S ALA* 4.1 11.2 - - + -
57S PHE* 3.6 38.4 - - + -
61S VAL* 5.2 4.5 - - + -
62S LYS 4.1 4.0 - - - +
75S ILE 4.2 1.8 - - - +
76S VAL* 1.3 77.0 - - - +
78S PHE* 1.3 62.1 + - - +
79S GLY 3.2 16.8 + - - +
80S SER 4.5 1.8 - - - +
81S ASP* 3.7 31.4 - - + -
84S VAL* 4.4 15.0 - - + -
241S ALA* 3.9 4.0 - - - +
243S PRO* 3.5 21.0 - - - +
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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