Contacts of the strand formed by residues 113 - 120 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A CYS 3.8 0.3 - - - +
22A GLU* 3.3 1.8 - - - -
23A LEU* 2.7 40.9 + - + +
49A ILE* 3.5 29.8 - - + -
50A CYS 3.4 9.6 - - - +
51A LEU* 3.9 7.4 - - + -
60A HIS* 3.6 22.4 - - + -
62A VAL* 4.0 12.8 - - + -
83A LEU* 4.8 4.7 - - + -
106A LEU* 3.6 29.2 - - + -
111A GLY* 4.2 1.6 - - - -
112A PRO* 1.3 78.1 - - - +
114A PHE* 1.3 66.3 + - - +
115A LEU* 4.7 3.4 - - + -
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Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A CYS 3.5 3.8 - - - -
22A GLU* 3.4 47.1 - - + -
49A ILE* 3.3 11.8 - - - +
50A CYS* 2.7 39.8 + - + +
51A LEU 4.5 0.4 - - - -
52A GLY* 3.7 26.7 - - - -
112A PRO* 4.1 9.2 - - + -
113A VAL* 1.3 74.2 - - - +
115A LEU* 1.3 63.8 + - - +
61E ARG* 3.4 28.5 - - - -
77E PRO 6.0 1.8 - - - -
79E THR* 3.5 45.3 - - + +
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TRP* 3.8 17.5 - - + -
20A GLY* 3.1 4.9 - - - -
21A CYS* 2.8 38.2 + - + +
23A LEU* 3.7 32.5 - - + -
46A LEU* 4.0 13.7 - - + -
48A THR 3.6 4.9 - - - +
49A ILE* 4.0 19.5 - - + -
62A VAL* 4.8 4.5 - - + -
104A PHE* 3.6 40.8 - - + -
113A VAL* 4.4 8.1 - - + +
114A PHE* 1.3 81.2 - - - +
116A SER* 1.3 63.1 + - - +
78E VAL* 4.3 1.9 - - - +
79E THR 4.6 4.2 + - - +
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 5.8 1.1 - - - -
19A TRP* 3.5 10.5 - - - -
46A LEU* 3.6 9.4 - - - +
47A HIS* 2.8 26.1 + - - +
48A THR* 2.7 36.5 + - - +
115A LEU* 1.3 73.0 - - - +
117A GLY* 1.3 60.8 + - - +
78E VAL* 3.5 13.9 - - - -
79E THR 3.4 21.8 - - - -
80E ILE* 4.3 9.1 - - - +
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.4 6.0 - - - +
19A TRP* 2.8 38.1 + - - +
45A LEU 2.9 14.1 - - - -
47A HIS* 3.7 13.9 + - - -
116A SER* 1.3 79.3 - - - +
118A GLN* 1.3 68.2 + - - +
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR* 4.4 18.0 - - - +
17A VAL 3.2 13.2 - - - +
18A LEU* 4.1 13.5 - - + +
19A TRP 4.2 0.4 - - - +
43A ARG 3.6 0.3 - - - +
44A LEU* 3.6 4.3 - - - +
45A LEU* 2.7 54.0 + - + +
47A HIS* 2.9 27.2 + - + -
117A GLY* 1.3 79.3 - - - +
119A GLU* 1.3 62.1 + - - +
43E ARG* 4.6 5.4 + - - +
97E GLN* 2.7 32.7 + - - +
98E LEU* 4.0 16.3 - - - +
99E SER* 5.0 2.0 + - - +
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR* 3.0 20.3 + - - -
17A VAL* 2.7 50.3 + - + +
18A LEU 4.9 1.0 - - - +
19A TRP* 3.8 25.4 - - + +
32A PHE* 3.4 38.2 - - + -
34A PRO 4.7 9.6 - - - -
43A ARG 3.6 6.1 - - - -
44A LEU* 4.6 1.6 - - + -
118A GLN* 1.3 71.5 - - - +
120A ARG* 1.3 59.1 + - - +
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR* 4.0 26.5 - - - +
42A CYS* 3.6 27.9 + - - +
43A ARG* 2.9 27.8 + - + +
45A LEU* 4.2 32.3 - - + -
97A GLN* 4.6 15.1 + - - +
118A GLN* 5.9 0.2 - - + -
119A GLU* 1.3 75.9 - - - +
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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