Contacts of the strand formed by residues 34 - 39 (chain C) 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 ILE 34 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 4.7 11.0 - - + -
22C CYS* 5.1 4.9 - - - -
24C ALA* 5.7 0.7 - - + -
27C TYR* 3.5 22.7 - - - +
29C PHE* 4.6 10.3 - - + -
32C TYR 4.5 3.4 - - - +
33C TRP* 1.3 84.0 - - - +
35C ASN* 1.3 63.3 + - - +
36C TRP* 3.3 33.8 - - + +
50C ASN* 3.3 4.0 - - - -
51C ILE* 3.1 39.4 + - + +
53C PRO* 5.0 2.7 - - + -
79C ALA* 4.4 18.4 - - + -
96C CYS* 4.2 11.9 - - + -
97C THR 3.3 11.9 - - - +
98C ARG* 4.6 6.1 - - + -
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Residues in contact with ASN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLU* 5.0 1.0 + - - -
96B TYR* 3.3 13.8 - - - -
33C TRP* 3.9 20.2 - - - +
34C ILE* 1.3 76.2 - - - +
36C TRP* 1.3 62.8 + - - +
47C TRP* 2.7 25.6 + - - +
49C GLY 3.8 2.5 - - - -
50C ASN* 3.3 15.3 + - - +
97C THR* 2.8 55.7 + - - +
98C ARG* 5.8 1.6 - - - +
104C TRP* 4.2 17.9 - - - +
105C PHE* 3.6 18.1 - - + +
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Residues in contact with TRP 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C GLN* 4.2 10.5 - - - -
20C LEU* 3.6 35.4 - - + -
21C SER 4.4 1.1 - - - -
22C CYS* 3.7 24.0 - - + -
34C ILE* 3.3 28.5 - - + +
35C ASN* 1.3 72.8 - - - +
37C VAL* 1.3 55.0 + - - +
47C TRP* 4.0 3.0 - - - -
48C VAL* 2.6 50.8 + - + +
49C GLY 3.1 13.4 + - - +
51C ILE* 4.5 6.6 - - + +
70C LEU* 4.1 20.1 - - + +
71C THR 5.9 0.2 + - - -
79C ALA* 3.7 23.3 - - + +
80C TYR 5.0 0.4 - - - -
81C MET* 3.5 43.5 - - + -
94C TYR* 4.7 6.3 - - + -
95C TYR 3.4 11.0 - - - -
96C CYS* 3.9 17.3 - - + -
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B PHE* 4.4 9.4 - - + -
35C ASN 4.6 0.2 - - - +
36C TRP* 1.3 75.9 - - - +
38C LYS* 1.3 66.0 - - - +
45C LEU* 3.8 20.0 - - + -
46C GLU 3.3 30.1 - - - +
47C TRP* 4.5 3.4 - - - -
48C VAL* 4.0 1.3 - - - -
94C TYR* 3.7 3.2 - - - +
95C TYR* 2.9 39.9 + - + +
97C THR* 4.0 9.6 - - + -
105C PHE* 4.8 7.2 - - + -
108C TRP* 3.5 33.0 - - + -
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Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 1.3 73.5 - - - +
39C GLN* 1.3 66.6 + - - +
40C ARG* 4.1 17.0 - - - +
45C LEU 3.8 0.3 - - - -
46C GLU* 3.0 52.9 + - + +
48C VAL* 3.6 11.1 - - + +
64C PHE* 4.0 21.6 - - + -
89C GLU* 3.2 36.1 + - - -
90C ASP* 3.8 11.3 + - - -
92C ALA* 4.4 6.3 - - + -
93C VAL 3.5 4.5 - - - -
94C TYR* 3.3 46.9 + - + +
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Residues in contact with GLN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLN* 3.0 41.1 + - - -
85B ASP* 5.8 0.2 + - - -
87B HIS* 4.6 1.8 + - - -
38C LYS* 1.3 77.9 - - - +
40C ARG* 1.3 67.3 + - - +
42C GLY* 5.8 1.7 - - - +
43C GLN 3.0 28.1 + - - +
44C GLY 4.1 4.7 - - - +
45C LEU* 3.4 24.8 - - + +
92C ALA* 3.8 4.4 - - - -
93C VAL* 2.9 51.5 + - + +
95C TYR* 3.4 20.9 + - + -
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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