Contacts of the strand formed by residues 88 - 95 (chain E) in PDB entry 1FYT
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 SER 88 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E ARG* 3.4 19.5 + - - +
37E GLN 3.3 3.3 + - - -
38E ASP* 2.7 32.4 + - - -
86E GLN 3.2 7.0 + - - -
87E THR* 1.3 79.0 - - - +
89E MET* 1.3 74.9 + - - +
90E TYR* 3.6 14.1 - - - -
113E ARG* 3.9 13.6 + - - +
114E LEU 2.9 30.9 + - - +
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Residues in contact with MET 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ARG 4.4 1.8 - - - +
36E ARG* 3.2 2.1 - - - -
37E GLN* 2.7 52.6 + - + +
88E SER* 1.3 80.6 + - - +
90E TYR* 1.3 66.6 + - - +
91E LEU* 4.4 12.1 - - + -
110E SER 4.9 3.6 - - - +
111E GLY* 3.4 10.5 - - - +
112E THR* 2.9 21.3 - - - +
113E ARG* 2.9 70.3 - - + +
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Residues in contact with TYR 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E GLN* 3.0 17.0 - - - +
21E LEU* 3.5 18.4 - - + -
34E TRP* 3.6 18.6 - - + -
35E TYR 3.2 7.2 - - - +
36E ARG* 4.0 7.8 + - + -
46E ILE* 3.6 17.3 - - + -
65E TYR* 3.1 41.6 + + - -
77E LEU* 3.6 18.2 - - + -
79E LEU* 4.3 2.2 - - + +
86E GLN* 2.5 32.0 + - - +
88E SER* 3.6 25.8 - - - -
89E MET* 1.3 72.7 - - - +
91E LEU* 1.3 61.5 + - - +
111E GLY* 3.3 2.6 - - - -
112E THR* 3.1 23.2 + - - +
114E LEU* 3.8 17.5 - - + -
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Residues in contact with LEU 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D GLN* 6.0 0.4 - - - +
43D LEU* 3.9 20.4 - - + -
6E GLN* 3.9 0.7 - - - +
33E PHE 3.8 0.3 - - - +
34E TRP* 3.4 5.0 - - - -
35E TYR* 2.7 47.5 + - + +
37E GLN* 3.6 25.6 - - + +
43E LEU* 3.9 25.4 - - + -
89E MET* 3.9 12.5 + - + -
90E TYR* 1.3 74.7 - - - +
92E CYS* 1.3 60.5 + - - +
108E PHE* 4.4 17.9 - - + -
109E GLY 4.1 12.1 - - - +
110E SER 4.6 2.0 - - - +
111E GLY* 3.7 23.8 - - - -
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Residues in contact with CYS 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 4.2 2.3 - - - +
6E GLN* 3.1 17.6 - - - +
23E CYS* 2.0 54.1 - - + -
32E MET* 4.3 7.2 - - - -
33E PHE 3.2 13.5 - - - +
34E TRP* 3.8 15.9 - - + -
75E PHE* 5.3 0.2 - - - -
91E LEU* 1.3 75.5 - - - +
93E ALA* 1.3 71.0 + - - +
108E PHE* 3.6 4.2 - - - -
109E GLY* 2.9 26.9 + - - -
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Residues in contact with ALA 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 5.0 1.1 - - - -
32E MET* 3.1 3.8 - - - +
33E PHE* 2.7 40.3 + - + +
35E TYR* 4.7 4.5 - - + -
92E CYS* 1.3 79.9 - - - +
94E SER* 1.3 60.5 + - - +
106E TYR* 3.6 36.1 - - + -
107E THR 3.4 11.9 - - - +
108E PHE* 3.9 13.0 - - + -
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Residues in contact with SER 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 3.4 23.8 - - - +
25E GLN* 4.0 6.7 - - - +
27E MET* 3.8 2.9 - - - +
29E HIS* 2.6 33.2 + - - +
31E ASN 3.0 12.6 - - - -
32E MET* 3.7 15.5 - - - -
33E PHE* 4.6 1.3 - - - -
93E ALA* 1.3 76.1 - - - +
95E SER* 1.3 66.8 + - - +
105E GLY 4.2 0.2 - - - +
106E TYR* 3.7 1.4 - - - -
107E THR* 3.2 26.9 + - - -
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Residues in contact with SER 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ASN* 2.7 33.4 + - - -
29E HIS* 3.2 20.3 + - - +
31E ASN* 2.8 32.5 + - - +
33E PHE* 3.6 12.8 - - - -
94E SER* 1.3 78.9 - - - +
96E SER* 1.3 60.9 + - - +
104E TYR* 5.0 0.7 - - - -
105E GLY 3.9 23.3 - - - -
106E TYR* 4.1 3.4 - - - -
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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