Contacts of the strand formed by residues 42 - 49 (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 GLY 42 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89D PHE* 3.7 15.9 - - - -
107D GLY 3.7 8.7 - - - -
108D THR 3.2 18.3 + - - -
36E ARG 3.4 4.2 - - - +
37E GLN* 3.6 1.9 - - - -
38E ASP* 3.1 27.4 + - - +
40E GLY 4.4 0.4 - - - +
41E LEU* 1.3 81.9 - - - +
43E LEU* 1.3 63.8 + - - -
44E ARG* 3.8 0.9 + - - +
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Residues in contact with LEU 43 (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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43D LEU* 3.6 28.7 - - + -
89D PHE* 4.6 7.1 - - + -
106D PHE* 3.5 58.5 + - + +
107D GLY 4.0 4.9 + - - -
35E TYR* 3.9 17.7 - - + -
36E ARG 3.5 3.4 - - - +
37E GLN* 3.3 46.9 - - + +
41E LEU 3.5 0.9 + - - +
42E GLY* 1.3 72.6 - - - -
44E ARG* 1.3 64.4 + - - +
45E LEU 4.3 0.3 + - - -
91E LEU* 3.9 16.4 - - + -
108E PHE* 4.4 6.7 - - + -
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Residues in contact with ARG 44 (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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35E TYR* 3.2 5.9 - - - -
36E ARG* 3.2 67.5 + - - +
38E ASP* 3.3 10.5 + - - -
41E LEU* 3.7 54.4 - - - +
42E GLY 4.6 0.2 - - - +
43E LEU* 1.3 77.9 - - - +
45E LEU* 1.3 63.6 + - - +
46E ILE* 3.4 4.2 + - - +
59E ASP* 5.9 2.9 - - + -
60E ILE* 3.6 38.4 - - + +
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Residues in contact with LEU 45 (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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103D LYS* 3.9 25.6 - - + +
104D LEU 4.8 4.5 - - - +
105D THR* 6.1 0.4 - - - +
33E PHE* 3.8 9.2 - - + -
34E TRP 3.5 15.9 - - - +
35E TYR* 3.5 39.0 - - + +
43E LEU 4.3 0.2 + - - -
44E ARG* 1.3 70.0 - - - +
46E ILE* 1.3 58.8 + - - +
47E TYR 3.6 14.4 - - - +
48E PHE* 3.5 29.6 - - + -
58E GLY* 4.0 11.4 - - - -
59E ASP* 2.8 45.3 + - - +
60E ILE* 3.0 10.0 + - - +
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Residues in contact with ILE 46 (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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34E TRP* 2.8 21.5 + - + +
35E TYR 4.2 4.5 - - - -
36E ARG* 4.1 9.6 - - + -
44E ARG 3.9 10.3 - - - +
45E LEU* 1.3 73.1 - - - +
47E TYR* 1.3 73.5 + - + +
58E GLY* 2.9 19.1 + - - -
60E ILE* 3.8 20.4 - - + +
61E PRO* 3.7 8.0 - - - +
65E TYR* 3.6 46.9 - - + -
77E LEU* 4.1 12.3 - - + -
90E TYR* 3.6 37.9 - - + -
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Residues in contact with TYR 47 (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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34E TRP* 3.0 27.6 + - + +
45E LEU* 3.6 2.4 - - - +
46E ILE* 1.3 100.3 - - + +
48E PHE* 1.3 66.2 + - - +
55E LYS* 4.7 6.3 - - + -
56E GLU 3.5 25.4 - - - -
57E LYS* 3.7 36.5 - - + +
58E GLY 3.9 2.0 - - - +
61E PRO* 3.9 15.9 - - + +
65E TYR* 3.4 32.7 + - + -
66E SER* 4.2 8.0 - - - -
67E VAL* 3.8 40.4 - - + -
75E PHE* 4.2 1.8 - - + -
77E LEU* 5.1 3.1 - - + -
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Residues in contact with PHE 48 (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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57A GLN* 3.6 24.0 - - - -
103D LYS* 3.9 14.1 - - + -
32E MET 3.3 6.3 - - - +
33E PHE* 3.3 28.3 - + + -
45E LEU* 3.5 28.3 - - + -
47E TYR* 1.3 78.3 - - - +
49E SER* 1.3 63.8 + - - +
50E TYR* 3.6 45.5 - + - -
54E MET 3.9 0.2 - - - +
55E LYS* 3.9 1.6 - - - -
56E GLU* 3.0 58.1 + - + +
57E LYS 3.9 12.8 - - - -
58E GLY* 4.3 2.0 - - - -
75E PHE* 3.6 7.4 - - - -
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Residues in contact with SER 49 (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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31E ASN* 3.2 3.5 - - - -
32E MET 2.9 33.2 + - - +
48E PHE* 1.3 73.9 - - - +
50E TYR* 1.3 64.3 + - - +
51E ASP 2.6 29.3 + - - -
54E MET* 2.7 21.8 + - - -
69E ARG* 3.0 27.3 + - - +
75E PHE* 3.7 13.4 - - - -
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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