Contacts of the strand formed by residues 66 - 73 (chain B) in PDB entry 3TIW
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 GLU 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU* 3.6 23.8 - - + +
59B LEU 3.1 12.1 - - - +
60B LYS* 3.5 27.1 + - + -
64B ARG 4.2 8.3 - - - +
65B ARG* 1.3 85.8 + - - +
67B ALA* 1.3 64.1 + - - +
91B ASN* 4.6 7.8 - - - +
92B LEU* 3.6 4.5 - - - +
147B ARG* 3.4 48.1 + - - +
150B ASP* 4.4 5.2 - - - +
173B TYR* 5.1 3.8 - - - -
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Residues in contact with ALA 67 (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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57B VAL 3.8 0.2 - - - +
58B LEU* 3.6 4.0 - - - +
59B LEU* 2.7 42.2 + - + +
66B GLU* 1.3 75.4 - - - +
68B VAL* 1.3 66.6 + - - +
69B CYS* 4.2 7.6 - - - -
88B VAL* 4.7 5.2 - - + -
91B ASN* 4.8 9.9 - - + +
92B LEU* 3.6 27.4 - - + -
147B ARG* 4.7 2.5 - - - +
150B ASP* 4.9 6.7 - - - +
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 5.6 0.7 - - - -
56B THR* 4.5 14.4 - - + -
57B VAL 3.3 11.2 - - - +
58B LEU* 4.0 13.5 - - + -
67B ALA* 1.3 78.5 - - - +
69B CYS* 1.3 69.9 + - - +
105B CYS* 4.6 10.3 - - - -
108B VAL* 5.1 4.9 - - + -
145B PRO* 3.6 38.9 - - + +
146B ILE* 4.9 4.0 - - - +
147B ARG* 4.5 13.2 - - + +
150B ASP* 5.4 3.2 + - - +
173B TYR* 4.0 39.7 - - + -
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Residues in contact with CYS 69 (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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36B ASN 4.2 5.4 - - - -
37B SER* 3.4 16.2 - - - +
39B VAL* 4.0 25.4 - - + -
56B THR* 3.3 2.5 - - - -
57B VAL* 2.7 41.3 + - + +
59B LEU* 3.8 22.0 - - + -
67B ALA* 4.2 3.8 - - - -
68B VAL* 1.3 82.6 - - - +
70B ILE* 1.3 64.3 + - - +
88B VAL* 4.0 23.1 - - - -
145B PRO* 4.1 4.7 - - - -
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Residues in contact with ILE 70 (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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37B SER* 2.8 19.8 + - - +
38B VAL* 3.4 9.9 - - + +
39B VAL* 3.0 25.4 + - - +
54B GLY* 3.7 23.8 - - - +
55B ASP 3.4 4.3 - - - -
56B THR* 4.3 3.1 - - + -
69B CYS* 1.3 73.4 - - - +
71B VAL* 1.3 66.2 + - - +
72B LEU* 4.0 11.2 + - + -
142B ALA 5.3 0.4 - - - +
143B TYR 3.7 8.1 - - - +
145B PRO* 3.5 30.3 - - + -
629D LEU* 3.7 48.0 - - + +
630D ALA* 4.9 0.2 - - - -
633D ALA* 4.9 2.2 - - + -
636D ARG* 5.2 6.1 - - - +
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Residues in contact with VAL 71 (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 VAL* 3.5 13.9 - - + +
41B LEU* 3.7 35.7 - - + -
46B MET* 4.2 11.4 - - + -
51B LEU* 4.4 10.5 - - + -
52B PHE 3.7 15.5 - - - +
53B ARG* 3.5 3.5 - - - -
54B GLY* 2.9 28.9 + - - -
55B ASP* 2.9 32.0 + - + +
57B VAL* 3.9 18.8 - - + -
69B CYS 4.0 0.2 + - - -
70B ILE* 1.3 73.5 - - - +
72B LEU* 1.3 67.0 + - - +
102B ILE* 5.2 0.4 - - + -
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Residues in contact with LEU 72 (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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33B ASN* 4.8 1.1 - - - +
38B VAL* 3.8 27.8 - - + -
39B VAL 3.1 6.7 + - - -
40B SER* 3.2 9.7 + - - +
41B LEU 3.1 22.3 + - - -
46B MET* 4.0 4.9 - - - -
53B ARG* 4.4 7.0 - - + +
54B GLY 4.4 0.7 - - - +
70B ILE* 4.8 2.7 - - + -
71B VAL* 1.3 81.0 - - - +
73B SER* 1.3 69.3 + - - +
630D ALA* 4.1 28.7 - - + +
633D ALA* 4.2 18.6 - - + -
634D GLU* 4.1 20.9 - - + +
637D LEU* 4.2 25.1 - - + -
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B SER* 4.6 0.9 + - - -
41B LEU 3.3 7.6 - - - -
43B GLN* 3.6 32.2 + - - -
46B MET* 3.6 18.7 - - - +
53B ARG* 5.2 5.2 - - - +
72B LEU* 1.3 80.1 - - - +
74B ASP* 1.3 61.2 + - - +
75B ASP 5.4 0.2 + - - -
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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
------------------------------------------------------------
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