Contacts of the strand formed by residues 92 - 100 (chain F) in PDB entry 1FSK
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 ALA 92 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F LYS* 4.4 9.0 - - + -
39F GLN 3.3 17.0 - - - +
40F ARG* 3.5 18.8 - - + +
41F PRO* 4.6 4.3 - - - -
90F ASP 2.9 10.1 + - - +
91F SER* 1.3 77.0 - - - +
93F VAL* 1.3 61.8 + - - +
94F TYR* 3.6 11.5 - - + +
112F THR 3.4 0.9 - - - +
113F LEU* 3.5 11.1 - - - +
114F VAL* 2.8 34.4 + - - +
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Residues in contact with VAL 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F VAL 4.1 0.5 - - - +
38F LYS* 3.5 2.6 - - - +
39F GLN* 2.9 55.4 + - + +
40F ARG 5.6 1.1 - - - -
41F PRO* 5.6 1.1 - - + +
92F ALA* 1.3 77.2 - - - +
94F TYR* 1.3 64.1 + - - +
95F TYR* 3.9 24.7 + - + +
110F GLN 5.3 0.2 - - - +
111F GLY* 3.8 13.2 - - - -
112F THR 3.0 25.4 - - - +
113F LEU* 4.3 9.4 - - + +
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Residues in contact with TYR 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F GLN* 3.1 13.9 + - - -
20F LEU* 3.5 33.0 - - + -
36F TRP* 4.7 7.2 - + + -
37F VAL 3.7 3.1 - - - +
38F LYS* 3.3 49.3 + - + +
48F VAL* 4.9 0.7 - - + -
64F PHE* 5.6 0.4 - + - -
81F MET* 4.0 26.2 - - + -
83F VAL* 5.0 9.0 - - + +
90F ASP* 2.8 25.9 + - - +
92F ALA* 3.6 10.5 - - + -
93F VAL* 1.3 72.9 - - - +
95F TYR* 1.3 62.6 + - - +
112F THR* 2.9 31.1 + - - +
114F VAL* 3.4 32.5 - - + -
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Residues in contact with TYR 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E GLN* 3.8 4.0 + - - -
42E GLN 4.3 1.7 + - - -
43E SER* 3.2 40.5 + - - -
44E PRO* 4.0 6.3 - - + -
6F GLN* 3.3 4.5 - - - +
35F ASN 3.7 0.5 - - - +
36F TRP* 3.4 7.1 - - - -
37F VAL* 2.9 44.3 + - + +
39F GLN* 3.4 30.5 + - + -
45F LEU* 5.2 0.7 - - + -
93F VAL* 3.9 25.3 - - + +
94F TYR* 1.3 76.2 - - - +
96F CYS* 1.3 63.4 + - - +
97F THR* 4.4 0.4 - - + -
108F TRP* 3.6 30.1 - + + -
109F GLY 3.5 19.5 - - - +
110F GLN 3.6 12.3 - - - -
111F GLY* 3.5 10.3 - - - -
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Residues in contact with CYS 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LEU* 3.4 16.3 - - - +
6F GLN* 3.0 20.4 + - - -
22F CYS* 2.4 50.3 - - + -
34F ILE* 4.2 5.2 - - + -
35F ASN 3.6 4.0 - - - -
36F TRP* 3.9 24.7 - - + -
95F TYR* 1.3 74.5 - - - +
97F THR* 1.3 59.2 + - - +
109F GLY 2.9 24.6 + - - -
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Residues in contact with THR 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LEU* 3.5 5.6 - - - +
34F ILE* 3.3 10.6 - - - +
35F ASN* 2.8 48.0 + - - +
37F VAL* 4.0 9.9 - - + -
95F TYR 4.3 0.7 - - - +
96F CYS* 1.3 79.9 - - - +
98F ARG* 1.3 62.4 + - - +
105F PHE* 3.1 33.8 + - + -
107F TYR 3.3 12.3 - - - +
108F TRP* 3.7 32.5 - - + -
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Residues in contact with ARG 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D GLU* 4.4 0.2 - - - -
2F VAL* 3.8 20.8 - - - +
4F LEU* 3.6 17.0 - - + +
27F TYR* 3.3 53.1 - - + +
32F TYR* 3.5 44.3 + - + -
33F TRP 3.7 18.4 - - - +
34F ILE* 4.6 2.7 - - + -
35F ASN* 5.8 0.4 - - - +
97F THR* 1.3 78.3 - - - +
99F GLY* 1.3 96.8 + - - +
100F ALA* 3.8 11.7 - - - +
105F PHE 4.1 3.1 - - - -
106F ALA 3.1 3.3 + - - -
107F TYR* 2.8 43.2 + - + +
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Residues in contact with GLY 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D GLU* 3.0 21.6 + - - -
35F ASN* 5.7 1.2 - - - +
98F ARG* 1.3 102.2 + - - +
100F ALA* 1.3 63.5 + - - +
103F THR 3.5 11.9 - - - -
104F TRP* 3.7 2.8 - - - +
105F PHE 3.6 15.3 - - - +
106F ALA* 3.7 4.5 - - - -
107F TYR* 3.8 2.6 - - - -
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Residues in contact with ALA 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ILE 3.8 10.5 - - - -
45D GLU* 4.0 5.1 - - - +
46D GLY 3.5 2.1 + - - -
55E TYR* 4.9 5.4 - - + +
32F TYR* 5.6 0.2 - - - -
98F ARG* 3.8 14.8 - - - +
99F GLY* 1.3 77.8 - - - +
101F ARG* 1.3 69.3 + - + +
102F ASP 2.7 1.4 + - - -
103F THR* 2.7 27.3 + - - +
106F ALA* 3.8 17.4 - - + +
107F TYR* 4.1 7.0 - - + -
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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