Contacts of the strand formed by residues 31 - 44 (chain E) in PDB entry 3FFC
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 31 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E HIS* 4.2 1.9 - - - +
30E ALA* 1.3 80.1 - - - +
39E LEU* 1.3 64.8 + - - +
40E TYR* 3.3 31.4 - - + +
55E GLN* 3.7 20.0 - - + +
56E PHE 3.1 10.5 - - - +
57E GLN* 3.9 5.2 + - - -
80E ARG* 3.9 0.9 - - - -
106E SER* 3.2 8.7 - - - -
107E SER* 3.0 42.1 + - - +
108E PHE 3.5 10.6 + - - -
109E THR* 3.9 0.5 - - - -
110E TRP* 3.1 22.2 - - + -
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Residues in contact with LEU 39 (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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23E CYS* 3.8 22.0 - - - -
25E PRO* 3.8 15.5 - - + -
31E THR* 1.3 75.9 - - - +
40E TYR* 1.3 69.0 + - - +
41E TRP* 3.8 20.6 - - + +
55E GLN* 3.4 1.0 - - - -
56E PHE* 2.6 43.6 + - + -
80E ARG* 3.4 20.0 - - - +
85E VAL 3.7 16.8 - - - +
87E SER* 3.5 39.3 - - - +
105E ALA 3.3 8.3 - - - +
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Residues in contact with TYR 40 (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 THR* 3.3 16.4 - - + +
39E LEU* 1.3 77.7 - - - +
41E TRP* 1.3 62.1 + - - +
42E TYR* 3.7 19.3 - - + -
52E LEU* 3.9 11.7 - - + -
54E ILE 3.4 5.2 - - - -
55E GLN* 3.4 39.9 - - + -
104E CYS* 3.1 7.3 - - - +
105E ALA* 2.7 44.8 + - + +
106E SER 4.2 0.2 - - - -
107E SER* 2.8 35.2 + - - -
109E THR 3.4 9.2 + - - -
110E TRP* 3.5 8.7 - - + +
117E ASP 4.0 1.0 + - - -
119E GLN* 3.3 47.6 + - + +
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Residues in contact with TRP 41 (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* 4.0 12.3 - - - -
21E PHE* 3.6 46.0 - - + -
22E TRP 3.9 4.0 - - - -
23E CYS* 3.3 29.6 - - + -
39E LEU* 3.8 13.6 - - + +
40E TYR* 1.3 72.2 - - - +
42E TYR* 1.3 55.8 + - - +
52E LEU* 3.5 4.9 - - - +
53E LEU* 2.7 40.2 + - + +
54E ILE* 2.8 37.7 + - + -
56E PHE* 4.6 2.0 - + - -
78E ALA* 4.5 4.9 - - + -
87E SER* 3.0 23.9 + - - -
88E THR 4.3 0.8 - - - -
89E LEU* 3.5 34.9 - - + +
102E TYR* 4.2 9.2 - - + -
103E LEU 3.7 8.1 - - - -
104E CYS* 3.7 19.3 - - + -
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Residues in contact with TYR 42 (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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110D PHE* 3.7 18.1 + - - +
112D PHE* 4.0 17.7 - + - -
40E TYR* 3.7 18.3 - - + -
41E TRP* 1.3 76.9 - - - +
43E GLN* 1.3 59.5 + - - +
50E PRO* 3.6 24.5 - - + -
51E LYS 3.4 6.3 - - - -
52E LEU* 3.3 42.6 - - + +
53E LEU* 3.9 5.5 - - - +
102E TYR* 3.4 10.0 - - - +
103E LEU* 2.6 43.1 + - + +
105E ALA* 4.3 3.6 - - + -
119E GLN* 2.5 37.3 + - - -
121E PHE* 3.2 27.8 - + - -
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Residues in contact with GLN 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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42E TYR* 1.3 74.4 - - - +
44E GLN* 1.3 61.9 + - - +
45E ILE* 3.6 30.5 + - + +
49E GLY 4.1 1.4 - - - +
50E PRO* 3.6 1.5 - - - +
51E LYS* 3.0 35.6 + - + +
53E LEU* 3.8 20.2 - - + +
72E PRO* 5.6 2.9 - - - +
76E PHE* 4.2 7.9 - - - -
97E GLU 4.4 1.2 + - - -
98E ASP* 4.1 9.5 + - - +
100E ALA* 3.8 12.6 - - + +
101E VAL 3.7 2.7 - - - -
102E TYR* 2.9 41.6 + - + -
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Residues in contact with GLN 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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44D GLN* 2.5 45.2 + - - +
50D MET* 3.7 8.6 - - - +
99D PHE* 3.5 11.1 - - - -
43E GLN* 1.3 72.2 - - - +
45E ILE* 1.3 67.3 + - - +
46E LEU* 3.9 0.6 + - - -
48E GLN 3.0 28.6 + - - +
49E GLY* 3.8 7.6 - - - -
50E PRO* 4.2 10.3 - - + -
100E ALA* 3.3 4.7 - - - +
101E VAL* 2.7 51.9 + - + +
103E LEU* 3.7 16.9 - - + +
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Residues in contact with ILE 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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43E GLN* 3.6 37.6 + - + +
44E GLN* 1.3 77.3 - - - +
46E LEU* 1.3 78.5 + - + +
47E GLY 3.2 0.2 + - - -
48E GLN* 3.1 50.8 + - + +
49E GLY 5.1 0.2 + - - -
97E GLU 4.2 14.6 - - - +
99E SER 4.7 5.8 - - - +
100E ALA* 4.1 7.9 - - + -
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Residues in contact with LEU 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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44E GLN* 3.9 1.4 + - - -
45E ILE* 1.3 82.9 - - + +
47E GLY* 1.3 63.2 + - - +
48E GLN* 3.8 3.5 + - - +
99E SER 5.3 1.2 + - - -
100E ALA* 5.3 2.2 - - - +
126E ARG* 6.1 4.3 - - - +
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Residues in contact with GLY 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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97D MET* 5.7 8.3 - - - +
99D PHE* 6.1 0.2 - - - -
114D THR* 3.7 17.4 - - - +
45E ILE 3.2 0.4 + - - -
46E LEU* 1.3 79.4 - - - +
48E GLN* 1.3 64.7 + - - +
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Residues in contact with GLN 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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99D PHE* 3.6 10.2 - - - -
114D THR* 4.3 7.9 - - - +
44E GLN* 3.0 22.5 + - - +
45E ILE* 3.1 46.5 + - + +
46E LEU 4.1 2.9 - - - +
47E GLY* 1.3 83.3 + - - +
49E GLY* 1.3 68.5 + - - +
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Residues in contact with GLY 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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99D PHE* 3.2 21.2 - - - -
112D PHE* 4.5 2.7 - - - -
113D GLY 3.8 10.9 + - - -
114D THR* 4.3 2.0 + - - +
43E GLN 4.1 3.5 - - - +
44E GLN* 4.1 4.8 - - - -
48E GLN* 1.3 85.2 - - - +
50E PRO* 1.3 78.3 - - - +
51E LYS* 3.5 5.5 + - - +
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Residues in contact with PRO 50 (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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50D MET* 3.5 35.9 - - + -
99D PHE* 4.5 0.7 - - + -
110D PHE 5.1 0.5 - - - +
112D PHE* 3.5 46.2 + - + +
42E TYR* 3.6 30.0 - - + -
43E GLN 3.6 8.1 - - - +
44E GLN* 3.8 5.8 - - + +
49E GLY* 1.3 85.2 - - - +
51E LYS* 1.3 58.9 + - - +
103E LEU* 3.8 17.9 - - + -
121E PHE* 4.7 1.8 - - + -
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Residues in contact with LYS 51 (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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109D GLN* 4.6 8.1 - - - +
42E TYR* 3.4 3.6 - - - -
43E GLN* 3.0 34.7 + - + +
49E GLY 4.4 4.5 - - - +
50E PRO* 1.3 73.6 - - - +
52E LEU* 1.3 66.4 + - - +
53E LEU* 3.3 2.4 + - - +
70E GLN* 3.9 32.3 + - + +
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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