Contacts of the strand formed by residues 103 - 108 (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 THR 103 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D GLY* 3.0 17.6 + - - -
47D ASN* 3.9 7.0 - - + +
34E PHE* 4.7 9.9 - - + -
46E LEU* 3.8 13.6 - - + +
49E TYR* 2.9 45.4 - - + +
50E GLY 4.1 2.9 - - - +
55E TYR* 5.1 3.3 - - - -
99F GLY* 3.5 1.2 - - - -
100F ALA* 2.7 37.7 + - - +
101F ARG 4.3 3.1 + - - -
102F ASP* 1.3 78.7 - - - +
104F TRP* 1.3 75.3 + - - +
106F ALA* 4.6 3.3 - - - +
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Residues in contact with TRP 104 (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* 3.2 41.5 - - + -
46D GLY* 3.3 19.7 - - - -
47D ASN* 3.1 24.7 - - - +
50D PRO 3.7 3.3 + - - -
51D GLY* 3.6 22.0 - - - -
52D THR* 3.6 17.3 - - - -
34E PHE* 4.8 9.3 - + + -
46E LEU* 3.9 8.3 - - - +
91E SER* 3.4 29.9 + - - -
96E TYR* 3.5 24.6 + + + -
33F TRP* 3.9 15.5 - + + -
35F ASN* 4.2 14.4 - - - +
99F GLY* 3.7 2.9 - - - -
103F THR* 1.3 87.0 - - - +
105F PHE* 1.3 95.1 + + + +
106F ALA 3.2 3.6 + - - -
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Residues in contact with PHE 105 (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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34E PHE* 3.6 26.5 - + - -
36E PHE* 3.3 33.3 - + + -
46E LEU* 3.5 14.6 - - - +
96E TYR* 4.5 11.9 - + + -
98E PHE* 4.0 24.9 - + - -
35F ASN* 3.6 19.2 - - + +
37F VAL* 4.8 6.7 - - + -
47F TRP* 4.1 18.2 - + - -
97F THR* 3.1 36.5 + - + -
98F ARG 3.9 4.8 + - - -
99F GLY* 3.6 7.9 - - - +
104F TRP* 1.3 83.8 - - + +
106F ALA* 1.3 61.5 + - - +
107F TYR 3.3 1.8 - - - +
108F TRP* 3.0 25.6 + + - +
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Residues in contact with ALA 106 (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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46E LEU* 3.8 16.0 + - + +
55E TYR* 3.4 36.1 + - + +
98F ARG 3.1 2.6 + - - -
99F GLY 3.8 3.8 - - - -
100F ALA* 3.8 20.4 - - + +
103F THR* 4.6 2.9 - - - +
104F TRP 3.2 1.0 + - - -
105F PHE* 1.3 79.8 - - - +
107F TYR* 1.3 76.0 + - + +
108F TRP* 4.3 4.1 - - - -
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Residues in contact with TYR 107 (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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55E TYR* 4.1 12.2 + - - -
2F VAL* 3.2 55.7 - - + +
4F LEU* 4.3 9.2 - - + -
97F THR* 3.3 9.0 - - - -
98F ARG* 2.8 56.5 + - + +
99F GLY 3.8 9.6 - - - -
100F ALA* 4.1 5.2 - - + -
106F ALA* 1.3 99.6 + - + +
108F TRP* 1.3 65.1 + - - +
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Residues in contact with TRP 108 (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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36E PHE* 3.8 24.0 - + - -
43E SER* 4.1 11.6 + - - +
44E PRO* 3.6 59.0 + - + -
45E LYS* 5.1 2.2 - - - -
46E LEU 4.7 1.6 - - - +
98E PHE* 5.7 1.3 - + - -
4F LEU* 4.3 8.6 + - - +
37F VAL* 3.5 31.6 - - + -
45F LEU* 4.6 10.1 - - + -
95F TYR* 3.6 28.9 - + + -
96F CYS 3.8 2.0 - - - -
97F THR* 3.7 7.2 - - + -
105F PHE* 3.0 34.6 + + + -
106F ALA 4.3 2.7 - - - -
107F TYR* 1.3 84.9 - - - +
109F GLY* 1.3 70.1 + - - +
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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