Contacts of the strand formed by residues 100 - 108 (chain T) in PDB entry 6AVO
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 100 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46T CYS* 3.5 27.1 - - - -
47T VAL 3.6 3.4 - - - -
52T ASP* 3.6 33.9 - - + +
53T THR* 3.8 3.8 - - + +
56T PHE* 3.9 25.8 - - + -
88T LEU* 4.0 22.1 - - + +
98T TYR* 3.4 5.1 + - + +
99T HIS* 1.3 81.2 - - - +
101T ASN* 1.3 62.2 + - - +
102T LEU* 4.2 10.3 + - + +
118T MET* 4.4 1.0 - - - +
119T ASP 4.0 2.6 - - - +
120T TYR* 3.3 19.4 - - - +
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Residues in contact with ASN 101 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4T LEU* 4.3 0.2 - - - +
45T LEU 3.5 0.9 - - - +
46T CYS* 3.5 3.8 - - - -
47T VAL* 3.0 46.3 + - + +
48T GLY* 5.3 2.0 - - - -
99T HIS* 4.9 8.7 + - - -
100T VAL* 1.3 74.4 - - - +
102T LEU* 1.3 59.7 + - - +
118T MET 3.5 3.4 - - - -
119T ASP* 3.4 4.1 - - - +
120T TYR* 2.8 44.7 + - - +
132T HIS* 3.3 31.2 - - + +
133T GLY 5.8 1.6 - - - +
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Residues in contact with LEU 102 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4T LEU* 4.9 0.2 - - - -
44T LEU* 4.2 19.7 - - + -
45T LEU 3.1 4.7 - - - +
46T CYS* 3.4 38.8 - - + -
56T PHE* 3.8 12.8 - - + -
84T THR* 3.3 34.3 - - + -
100T VAL* 4.4 10.3 - - + +
101T ASN* 1.3 78.7 - - - +
103T LEU* 1.3 65.8 + - - +
104T LEU* 4.9 2.0 - - + +
118T MET* 3.0 45.5 + - + -
132T HIS* 2.9 20.9 + - - -
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Residues in contact with LEU 103 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4T LEU* 4.1 17.7 - - + -
5T ILE* 4.2 5.2 - - - +
6T GLY* 4.2 24.2 - - - +
15T VAL* 5.8 0.2 - - + -
45T LEU* 3.0 42.0 + - + +
102T LEU* 1.3 85.1 - - - +
104T LEU* 1.3 60.6 + - - +
105T ALA 3.3 4.7 + - - -
115T LEU* 4.5 12.1 - - + -
116T TYR 3.1 18.8 - - - +
117T TYR* 3.6 8.7 - - + -
130T ALA* 3.6 27.1 - - + -
131T ALA 4.6 0.9 - - - +
132T HIS* 3.3 26.2 - - + +
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Residues in contact with LEU 104 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T MET* 4.8 6.7 - - + -
42T ILE* 3.4 28.5 - - + -
43T LEU 3.4 10.8 - - - +
44T LEU* 3.8 23.8 - - + -
60T ILE* 5.4 0.7 - - + -
77T PRO* 4.2 22.2 - - + +
80T ALA* 4.1 30.1 - - + +
81T ALA* 4.2 13.0 - - + +
84T THR* 4.2 10.5 - - - +
102T LEU* 4.3 3.4 - - + +
103T LEU* 1.3 71.0 - - - +
105T ALA* 1.3 63.2 + - - +
106T GLY* 3.6 1.6 + - - -
116T TYR* 3.1 30.6 + - + -
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Residues in contact with ALA 105 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T VAL* 3.2 32.1 - - + -
15T VAL* 3.4 16.8 - - + -
42T ILE* 3.7 2.9 - - - +
43T LEU* 3.0 36.1 + - + +
45T LEU* 4.9 0.2 - - + -
103T LEU 3.3 3.4 + - - +
104T LEU* 1.3 74.2 - - - +
106T GLY* 1.3 57.8 + - - +
114T ALA 3.9 1.6 - - - -
115T LEU* 3.3 17.5 - - + +
183T ILE* 3.9 9.9 - - + +
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Residues in contact with GLY 106 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13T VAL* 3.7 6.2 - - - +
41T LYS 3.6 10.8 - - - -
42T ILE* 4.5 1.8 - - - -
77T PRO* 4.0 20.2 - - - -
104T LEU* 3.6 0.6 + - - -
105T ALA* 1.3 76.4 - - - +
107T TYR* 1.3 60.9 + - - +
113T PRO* 3.2 5.2 - - - +
114T ALA 3.0 34.1 + - - -
183T ILE* 4.6 3.8 - - - -
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Residues in contact with TYR 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11T ASP* 4.3 21.4 - - + +
12T TYR 4.8 0.2 - - - -
13T VAL* 5.7 0.2 - - + -
41T LYS* 3.3 34.2 + - + +
77T PRO* 3.8 6.6 - - - +
106T GLY* 1.3 74.7 - - - +
108T ASP* 1.3 72.2 + - - +
109T GLU* 4.7 8.2 + - - -
112T GLY* 3.7 7.7 - - - -
113T PRO* 3.3 45.3 - - + -
183T ILE* 3.8 21.5 - - + +
184T ASP 3.5 18.8 - - - +
185T LYS* 3.3 40.0 - - + +
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Residues in contact with ASP 108 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141O LYS* 5.5 2.4 + - - -
41T LYS* 5.4 0.2 - - - -
76T SER* 3.8 22.4 - - - -
77T PRO* 3.6 21.6 - - + +
107T TYR* 1.3 86.6 - - - +
109T GLU* 1.3 67.2 + - - +
110T HIS* 2.7 36.5 + - - +
111T GLU* 3.0 20.8 + - + +
112T GLY* 3.3 25.8 + - - +
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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