Contacts of the strand formed by residues 113 - 120 (chain F) in PDB entry 3T30
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 VAL 113 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F GLU* 3.4 1.7 - - - -
23F LEU* 2.7 58.3 + - + +
49F ILE* 3.4 31.4 - - + -
50F CYS 3.5 9.9 - - - +
51F LEU* 4.4 10.5 - - + -
60F HIS* 4.9 3.1 - - + -
62F VAL* 4.1 10.5 - - + -
83F LEU* 4.8 4.7 - - + -
106F LEU* 3.4 34.3 - - + -
111F GLY* 3.6 0.2 - - - -
112F PRO* 1.3 74.2 - - - +
114F PHE* 1.3 65.7 + - - +
115F LEU* 4.0 7.0 - - + +
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Residues in contact with PHE 114 (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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21F CYS 3.2 8.7 - - - +
22F GLU* 3.5 37.2 - - + -
49F ILE* 3.3 6.8 - - - +
50F CYS* 2.8 44.1 + - + +
52F GLY* 3.7 27.4 - - - -
112F PRO* 4.0 18.2 - - + -
113F VAL* 1.3 70.2 - - - +
115F LEU* 1.3 71.5 + - - +
61G ARG* 3.8 28.3 - - - -
77G PRO 5.7 3.6 - - - -
79G THR* 3.5 43.5 - - + +
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Residues in contact with LEU 115 (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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19F TRP* 3.4 19.7 - - + -
20F GLY* 3.1 4.9 - - - -
21F CYS* 2.8 44.3 + - - +
23F LEU* 3.8 26.5 - - + -
46F LEU* 4.1 10.8 - - + -
48F THR 3.4 5.8 - - - +
49F ILE* 3.7 30.3 - - + -
62F VAL* 4.4 5.2 - - + -
104F PHE* 4.1 26.7 - - + -
113F VAL* 4.0 15.7 - - + +
114F PHE* 1.3 84.7 - - - +
116F SER* 1.3 62.0 + - - +
78G VAL* 4.5 1.7 - - - +
79G THR 4.5 3.9 + - - +
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Residues in contact with SER 116 (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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19F TRP* 3.6 10.8 - - - -
46F LEU* 3.4 10.2 - - - +
47F HIS* 2.8 26.3 + - - +
48F THR* 2.8 37.3 + - - +
115F LEU* 1.3 71.2 - - - +
117F GLY* 1.3 58.6 + - - +
78G VAL* 3.3 16.2 - - - -
79G THR 3.2 21.5 - - - -
80G ILE* 4.2 9.4 - - - +
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Residues in contact with GLY 117 (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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18F LEU* 3.8 7.1 - - - +
19F TRP* 2.9 36.5 + - - +
45F LEU 2.9 15.5 - - - -
47F HIS* 3.7 13.8 + - - -
116F SER* 1.3 76.8 - - - +
118F GLN* 1.3 67.9 + - - +
78G VAL* 4.8 0.4 - - - +
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Residues in contact with GLN 118 (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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16F THR* 3.8 26.8 - - + +
17F VAL 3.1 12.8 - - - +
18F LEU* 4.2 10.9 - - + +
19F TRP* 3.6 1.7 - - - +
44F LEU* 3.5 6.1 - - - +
45F LEU* 2.8 50.0 + - + +
47F HIS* 3.0 27.3 + - + -
117F GLY* 1.3 78.6 - - - +
119F GLU* 1.3 60.7 + - - +
120F ARG 3.7 0.5 + - - -
97G GLN* 2.7 33.3 + - - +
98G LEU* 3.8 16.6 - - - +
99G SER 5.0 1.6 - - - +
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Residues in contact with GLU 119 (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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16F THR* 3.3 6.9 - - - +
17F VAL* 2.7 55.4 + - + +
18F LEU 4.9 0.7 - - - +
19F TRP* 4.0 19.4 - - + +
32F PHE* 3.4 36.8 - - + -
33F ARG 4.9 1.7 - - - +
34F PRO 5.1 0.2 - - - -
35F GLN* 3.1 46.1 + - - +
43F ARG 3.7 5.8 - - - +
44F LEU* 4.5 1.3 - - + -
118F GLN* 1.3 74.3 - - - +
120F ARG* 1.3 59.4 + - - +
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Residues in contact with ARG 120 (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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16F THR* 4.1 19.5 - - + +
35F GLN* 4.2 17.5 + - - +
42F CYS* 3.4 28.8 - - - +
43F ARG* 3.2 58.1 + - + +
45F LEU* 4.5 21.3 - - + -
97F GLN* 3.4 24.4 + - - +
118F GLN 3.7 1.0 + - - -
119F GLU* 1.3 75.8 - - - +
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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