Contacts of the helix formed by residues 69 - 74 (chain B) in PDB entry 3T06
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 LEU 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A CYS* 6.1 0.7 - - + -
879A MET* 3.5 33.1 - - + +
883A THR* 4.1 21.8 - - + -
917A LEU* 4.4 18.6 - - + +
920A VAL* 4.2 17.5 - - + +
921A ASN* 3.3 26.0 + - - +
924A VAL* 4.4 10.3 - - + -
63B GLN* 4.2 0.8 - - + +
66B TYR* 2.7 35.0 + - + +
68B ARG* 1.3 78.2 - - - +
70B ARG* 1.3 67.3 + - - +
71B PRO* 3.1 3.4 - - - -
72B LEU* 2.9 27.2 + - + +
73B SER* 5.2 0.2 - - - -
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 5.4 6.9 - - + +
63B GLN* 2.6 57.9 + - + +
64B GLU* 3.0 20.3 + - - -
66B TYR 3.1 11.8 + - - +
67B ASP* 2.9 34.9 + - - +
69B LEU* 1.3 80.1 - - - +
71B PRO* 1.4 63.7 - - + +
73B SER* 3.1 30.0 + - - -
74B TYR* 3.8 10.0 - - + +
98B LYS* 3.8 15.7 - - - +
99B TRP* 3.5 24.9 - - - -
102B GLU* 2.9 40.0 + - - +
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Residues in contact with PRO 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928A GLU* 6.2 0.2 - - - +
67B ASP 3.1 24.5 - - - +
68B ARG* 3.5 13.9 - - - +
69B LEU 3.1 5.8 - - - +
70B ARG* 1.4 90.1 - - + +
72B LEU* 1.3 58.6 + - + -
73B SER 2.8 10.0 + - - -
74B TYR* 3.2 17.1 + - + +
75B PRO* 3.2 19.2 - - - +
102B GLU* 5.5 1.6 - - - +
106B PHE* 3.8 44.4 - - + -
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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
----------------------------------------------------------
833A CYS* 4.9 8.1 - - + +
836A GLN* 4.3 19.1 - - + +
837A SER* 4.0 17.3 - - - +
840A LEU* 6.0 2.1 - - - +
872A ARG* 5.9 0.3 + - - -
876A ILE* 3.2 25.0 - - + +
879A MET* 4.6 18.6 - - + -
924A VAL* 4.5 20.9 - - + -
928A GLU* 3.6 23.6 - - - +
58B TRP* 4.5 3.3 - - - -
68B ARG 4.0 12.3 - - - +
69B LEU* 2.9 20.3 + - + +
71B PRO* 1.3 77.9 - - + +
73B SER* 1.3 57.0 + - - +
74B TYR 3.5 0.8 + - - -
75B PRO* 3.9 9.6 - - - +
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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
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876A ILE* 4.1 7.8 - - - +
879A MET* 5.3 0.2 - - - -
880A GLN* 4.5 2.4 + - - -
7B LYS* 3.6 10.9 + - - -
9B VAL* 3.5 22.3 - - - +
58B TRP* 3.8 22.0 - - - -
59B ASP 4.7 0.9 + - - -
60B THR* 4.3 16.6 - - - +
63B GLN* 3.6 23.2 + - - -
69B LEU 5.3 0.2 + - - -
70B ARG 3.1 15.7 + - - -
71B PRO 2.8 1.0 - - - -
72B LEU* 1.3 79.2 - - - +
74B TYR* 1.3 63.8 + - - +
75B PRO* 3.7 1.1 - - - -
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Residues in contact with TYR 74 (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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9B VAL* 4.1 12.3 - - + -
11B VAL* 3.7 32.2 - - + +
60B THR* 5.2 2.1 - - + +
70B ARG* 3.8 15.9 - - + -
71B PRO* 3.5 28.3 - - + +
73B SER* 1.3 83.0 - - - +
75B PRO* 1.3 69.2 - - + +
76B ASP 3.5 0.5 + - - -
77B THR* 2.9 25.2 + - - -
80B ILE* 4.4 7.0 - - + -
99B TRP* 3.9 2.6 - - - -
102B GLU* 2.5 42.8 + - + +
103B VAL* 4.2 10.1 - - + +
106B PHE* 3.6 29.0 - + + +
107B CYS* 3.8 23.5 - - - -
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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
------------------------------------------------------------
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