Contacts of the strand formed by residues 113 - 120 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLU* 3.4 1.5 - - - -
23B LEU* 2.6 46.7 + - + +
49B ILE* 3.5 30.1 - - + -
50B CYS 3.5 8.5 - - - +
51B LEU* 3.7 11.9 - - + -
60B HIS* 3.5 34.5 - - + -
62B VAL* 4.1 12.8 - - + -
83B LEU* 4.8 1.3 - - + -
106B LEU* 3.7 19.3 - - + -
111B GLY* 4.1 1.8 - - - -
112B PRO* 1.3 73.4 - - - +
114B PHE* 1.3 66.1 + - - +
115B LEU* 4.1 4.5 - - + +
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Residues in contact with PHE 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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61A ARG* 3.6 32.1 - - - -
63A GLU* 5.6 0.7 - - - -
77A PRO 5.7 3.8 - - - -
79A THR* 3.5 42.4 - - + +
21B CYS 3.2 7.9 - - - +
22B GLU* 3.4 46.4 - - + -
48B THR 4.7 0.2 - - - -
49B ILE* 3.3 9.7 - - - +
50B CYS* 2.8 42.2 + - + +
51B LEU 4.5 0.2 - - - -
52B GLY* 3.8 25.1 - - - -
112B PRO* 4.1 9.4 - - + -
113B VAL* 1.3 73.9 - - - +
115B LEU* 1.3 64.1 + - - +
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Residues in contact with LEU 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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78A VAL* 4.5 1.2 - - - +
79A THR 4.4 6.1 + - - +
19B TRP* 4.0 9.0 - - + -
20B GLY* 3.1 4.9 - - - -
21B CYS* 2.8 47.9 + - - +
23B LEU* 3.8 29.2 - - + -
46B LEU* 4.2 9.6 - - + -
48B THR 3.4 6.1 - - - +
49B ILE* 4.0 21.8 - - + -
62B VAL* 4.6 4.5 - - + -
104B PHE* 3.6 45.5 - - + -
113B VAL* 4.1 11.0 - - + +
114B PHE* 1.3 82.3 - - - +
116B SER* 1.3 61.3 + - - +
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Residues in contact with SER 116 (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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78A VAL* 3.4 14.6 - - - -
79A THR 3.3 21.5 - - - -
80A ILE* 4.2 9.7 - - - +
18B LEU* 6.4 0.2 - - - -
19B TRP* 3.5 11.2 - - - -
46B LEU* 3.5 9.2 - - - +
47B HIS* 2.9 26.9 + - - +
48B THR* 2.7 40.1 + - - +
115B LEU* 1.3 71.9 - - - +
117B GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 117 (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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18B LEU* 3.8 7.4 - - - +
19B TRP* 2.8 36.4 + - - +
45B LEU 2.8 14.6 - - - -
47B HIS* 3.7 13.8 + - - -
116B SER* 1.3 78.0 - - - +
118B GLN* 1.3 69.5 + - - +
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Residues in contact with GLN 118 (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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97A GLN* 2.7 33.0 + - - +
98A LEU* 4.0 12.0 - - - +
99A SER 5.0 0.7 + - - -
16B THR* 4.1 19.6 + - - +
17B VAL 3.2 15.0 - - - +
18B LEU* 4.1 11.7 - - + +
19B TRP* 4.2 3.3 - - - +
43B ARG 3.7 0.2 - - - +
44B LEU* 3.6 2.7 - - - +
45B LEU* 2.7 59.4 + - + +
47B HIS* 3.0 28.9 + - + -
117B GLY* 1.3 80.6 - - - +
119B GLU* 1.3 67.1 + - - +
120B ARG 3.8 0.5 + - - -
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Residues in contact with GLU 119 (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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15B THR 3.8 0.7 - - - +
16B THR* 3.1 6.1 - - - -
17B VAL* 2.8 56.3 + - + +
18B LEU 4.9 0.7 - - - +
19B TRP* 3.8 24.7 - - + +
32B PHE* 3.5 31.3 - - + -
41B SER* 3.1 31.4 + - - +
43B ARG 3.6 6.1 - - - -
44B LEU* 4.8 2.0 - - + +
118B GLN* 1.3 73.6 - - - +
120B ARG* 1.3 58.3 + - - +
121B TYR* 4.5 0.8 + - - -
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Residues in contact with ARG 120 (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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15B THR 3.9 4.3 - - - -
16B THR* 3.6 20.9 - - + -
41B SER 3.2 4.4 + - - +
42B CYS* 3.2 1.9 + - - +
43B ARG* 3.0 40.7 + - + +
45B LEU* 3.9 31.4 - - + -
97B GLN* 4.7 15.3 + - - +
118B GLN 3.8 0.2 + - - -
119B GLU* 1.3 74.2 - - - +
121B TYR* 1.3 69.5 + - - +
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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