Contacts of the helix formed by residues 101 - 115 (chain B) in PDB entry 1FZY
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 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 4.4 7.4 - - - +
10B GLU* 3.4 16.2 - - - +
13B ALA* 5.0 11.4 - - + -
62B TYR* 4.5 1.6 - - - -
96B TRP* 4.8 0.9 - - - -
99B VAL 3.6 8.3 + - - +
100B ILE* 1.3 78.8 - - - +
102B LEU* 1.3 59.5 + - - +
103B LYS* 3.4 16.4 + - - +
104B SER* 3.0 26.3 + - - -
105B ALA* 2.9 29.0 + - - +
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 6.2 1.1 - - + -
10B GLU* 3.0 31.4 + - + +
14B VAL* 5.4 0.2 - - - -
24B LEU* 3.9 29.4 - - + -
35B LEU* 4.8 7.4 - - + -
56B ILE* 4.1 22.2 - - + -
58B VAL* 4.4 16.8 - - + -
62B TYR* 3.5 20.9 - - + +
67B PRO* 3.8 33.4 - - + -
69B MET* 4.8 4.0 - - + +
96B TRP* 5.0 1.1 - - + -
101B THR* 1.3 70.8 - - - +
103B LYS* 1.3 63.7 + - - +
105B ALA* 3.7 4.0 - - + +
106B LEU* 2.9 32.1 + - - +
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 4.5 1.4 + - - -
13B ALA* 3.9 19.4 + - + +
14B VAL* 3.9 27.4 - - + +
17B ASP* 2.8 45.0 + - + +
20B ALA* 4.5 4.9 - - + -
22B ILE* 4.2 17.4 - - + +
101B THR* 3.1 14.0 + - - +
102B LEU* 1.3 77.4 - - - +
104B SER* 1.3 59.4 + - - +
106B LEU* 3.2 9.3 + - - +
107B ILE* 2.9 44.5 + - + +
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Residues in contact with SER 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL 5.0 0.2 + - - -
100B ILE* 3.3 13.0 - - - +
101B THR* 3.0 31.6 + - - -
103B LYS* 1.3 80.4 - - - +
105B ALA* 1.3 60.1 + - - +
107B ILE* 3.3 16.1 + - - +
108B SER* 2.9 27.5 + - - -
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B MET* 4.0 24.4 - - - +
89B LEU* 5.1 0.7 - - + +
91B ILE* 4.5 7.9 - - + -
92B LEU* 5.0 0.7 - - + -
96B TRP* 4.6 9.4 - - + -
100B ILE* 4.3 12.3 - - + -
101B THR 2.9 17.5 + - - +
102B LEU* 3.7 9.2 - - + +
104B SER* 1.3 76.4 + - - +
106B LEU* 1.3 62.8 - - - +
108B SER* 2.7 26.1 + - - -
109B LEU* 3.1 12.0 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.4 37.7 - - + -
23B THR 4.3 1.1 - - - +
24B LEU* 4.6 6.5 - - + -
37B GLY* 3.9 27.4 - - - -
38B THR 4.6 0.4 - - - +
39B PHE* 3.9 15.3 - - + -
54B VAL* 4.1 26.0 - - + -
56B ILE* 4.5 6.7 - - + -
69B MET* 3.6 23.3 - - + -
102B LEU 2.9 28.8 + - - +
103B LYS* 3.4 4.9 - - - +
105B ALA* 1.3 74.3 - - - +
107B ILE* 1.3 64.1 + - - +
109B LEU* 3.2 18.2 + - + +
110B GLN* 3.2 9.9 + - - +
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASP* 5.2 1.6 - - - +
20B ALA* 4.5 12.3 - - + +
22B ILE* 4.3 14.1 - - + -
103B LYS* 2.9 41.1 + - + +
104B SER* 3.3 18.1 + - - +
106B LEU* 1.3 76.2 - - - +
108B SER* 1.3 56.6 + - - +
110B GLN* 3.2 20.5 + - + +
111B ALA* 3.1 24.1 + - + +
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Residues in contact with SER 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 3.5 16.1 - - - +
91B ILE* 3.3 27.1 - - - +
104B SER 2.9 13.6 + - - -
105B ALA 2.7 17.7 + - - -
107B ILE* 1.3 76.0 - - - +
109B LEU* 1.3 61.3 + - - +
111B ALA* 3.3 9.7 + - - +
112B LEU* 2.9 25.8 + - - +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PHE* 3.8 13.5 - - + -
54B VAL* 3.9 38.4 - - + -
69B MET* 4.2 15.5 - - + -
71B PHE* 4.1 8.4 - - + -
87B ILE* 3.7 34.5 - - + -
89B LEU* 3.9 21.5 - - + -
92B LEU* 4.8 2.2 - - + -
105B ALA 3.1 10.8 + - - +
106B LEU* 3.2 13.0 + - + +
108B SER* 1.3 72.8 - - - +
110B GLN* 1.3 65.7 + - - +
111B ALA 3.1 0.2 - - - -
112B LEU* 3.2 10.0 + - + +
113B LEU* 3.0 28.2 + - - +
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Residues in contact with GLN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ALA 4.7 5.6 + - - +
22B ILE* 4.6 5.9 - - - +
39B PHE* 3.6 27.0 - - + +
40B LEU* 3.4 28.6 + - - +
41B GLY 4.9 0.4 + - - -
42B PRO* 3.6 30.0 - - + +
43B PRO* 5.2 4.4 - - - +
106B LEU 3.2 7.9 + - - +
107B ILE* 3.2 25.9 + - + +
109B LEU* 1.3 76.4 - - - +
111B ALA* 1.3 61.9 + - - +
113B LEU* 3.5 5.9 + - - +
114B GLN* 3.2 15.6 + - - +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ILE* 3.1 12.6 + - + +
108B SER* 3.5 12.8 - - - +
109B LEU 3.1 0.2 - - - -
110B GLN* 1.3 76.8 - - - +
112B LEU* 1.3 59.1 - - - +
114B GLN* 3.1 10.7 + - - +
115B SER* 2.8 30.8 + - - -
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B HIS* 3.0 23.7 + - + +
79B ASN* 3.8 37.9 - - + +
80B ILE* 4.8 7.6 - - + -
87B ILE* 4.0 26.7 - - + -
88B CYS 4.2 8.3 - - - +
89B LEU* 4.6 14.6 - - + -
108B SER 2.9 14.7 + - - +
109B LEU* 3.4 18.8 - - + +
111B ALA* 1.3 77.2 - - - +
113B LEU* 1.3 62.0 + - + +
115B SER 3.1 24.8 + - - +
117B GLU* 4.5 11.4 - - + +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PHE* 3.5 30.3 - - + -
42B PRO* 3.9 10.1 - - + -
45B THR* 4.9 1.7 - - - +
46B PRO* 5.8 0.2 - - - +
47B TYR* 3.5 38.7 - - + -
52B PHE* 3.9 25.8 - - + -
71B PHE* 4.8 2.9 - - + -
75B VAL* 4.5 8.3 - - + -
77B HIS* 3.4 20.3 - - + +
80B ILE* 3.7 30.1 - - + -
109B LEU 3.0 18.5 + - - +
110B GLN 3.6 7.2 - - - +
112B LEU* 1.3 77.5 - - + +
114B GLN* 1.3 62.6 + - - +
116B PRO* 3.8 4.2 - - - +
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Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A HIS* 5.0 14.2 + - - -
42B PRO* 3.8 18.3 - - + +
43B PRO* 4.2 9.5 + - - +
44B GLY 5.5 0.8 + - - -
45B THR* 4.0 24.5 - - + +
110B GLN 3.2 10.3 + - - +
111B ALA* 3.1 12.5 + - - +
113B LEU* 1.3 81.1 - - - +
115B SER* 1.3 68.0 + - - +
116B PRO* 3.4 7.4 - - - +
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ALA 2.8 15.3 + - - -
112B LEU* 3.2 12.0 - - - +
114B GLN* 1.3 87.0 + - - +
116B PRO* 1.3 68.1 - - - +
117B GLU* 3.6 12.6 + - - +
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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