Contacts of the strand formed by residues 112 - 117 (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 ILE 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ILE* 3.4 11.7 - - + +
82B MET* 3.9 35.9 - - + -
100B THR* 5.7 3.1 - - - -
103B VAL* 4.1 26.5 - - + -
104B LYS* 4.2 29.6 - - + -
107B CYS 5.9 0.2 - - - +
110B VAL 3.6 15.7 + - - +
111B PRO* 1.3 79.3 - - - +
113B ILE* 1.3 68.2 + - - +
114B LEU 4.5 0.2 - - - +
151B ILE* 4.5 17.5 - - + +
152B GLY 5.2 5.6 + - - +
153B ALA* 3.2 10.1 - - - +
154B PHE 2.8 30.5 + - - +
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Residues in contact with ILE 113 (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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79B VAL* 4.3 8.5 - - + -
80B ILE 2.9 9.5 + - - -
81B LEU* 3.1 32.6 - - + +
82B MET 3.1 21.7 + - - -
112B ILE* 1.3 79.1 - - - +
114B LEU* 1.3 60.8 + - - +
115B VAL* 3.4 16.1 + - + -
154B PHE* 4.2 25.6 - - + -
155B GLY 3.6 8.3 - - - +
157B MET* 4.4 8.1 - - + -
170B VAL* 4.2 14.4 - - + +
173B MET* 4.0 22.2 - - + -
174B ALA* 4.4 7.4 - - + -
177B ALA* 4.2 13.9 - - + -
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Residues in contact with LEU 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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82B MET* 3.3 23.8 - - + +
84B PHE* 4.0 17.7 - - + -
95B ILE* 3.9 25.1 - - + -
112B ILE* 4.0 2.6 + - - +
113B ILE* 1.3 69.7 - - - +
115B VAL* 1.3 59.6 + - - +
144B GLY 4.1 3.1 - - - +
147B MET* 3.8 21.8 - - + -
148B ALA* 3.5 37.2 - - + +
151B ILE* 3.9 10.8 - - + -
153B ALA* 4.2 5.5 - - + +
155B GLY 3.0 12.1 + - - +
156B TYR* 3.2 15.8 - - + -
157B MET 3.0 25.1 + - - -
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Residues in contact with VAL 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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21B LEU* 4.2 11.7 - - + -
81B LEU* 3.8 13.2 - - + -
82B MET 2.9 12.9 + - - +
83B CYS* 3.3 13.2 - - + -
84B PHE* 3.1 31.4 + - - +
113B ILE* 3.4 18.6 + - + +
114B LEU* 1.3 73.1 - - - +
116B GLY* 1.3 69.3 + - - +
117B ASN* 4.1 2.5 - - + +
157B MET 3.2 9.2 - - - +
159B CYS* 4.0 20.4 - - - -
170B VAL* 3.6 29.4 - - + -
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Residues in contact with GLY 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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84B PHE* 3.7 25.8 - - - -
86B ILE* 3.6 9.1 - - - +
115B VAL* 1.3 70.9 - - - +
117B ASN* 1.3 63.0 + - - -
156B TYR* 3.9 13.1 - - - -
157B MET 2.9 12.0 + - - -
158B GLU* 3.2 3.7 - - - -
159B CYS 2.9 26.5 + - - -
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Residues in contact with ASN 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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16B CYS 3.4 6.8 + - - +
17B GLY* 3.2 34.8 + - - -
20B CYS* 5.6 0.2 - - - +
21B LEU* 4.9 9.5 - - + +
83B CYS* 4.9 4.3 - - + -
84B PHE 3.0 21.2 + - - +
85B SER* 4.2 0.6 - - - +
86B ILE* 2.7 32.9 + - - +
115B VAL* 3.6 6.7 + - + -
116B GLY* 1.3 73.0 - - - +
118B LYS* 1.3 91.3 + - - +
119B LYS 3.4 1.3 - - - -
159B CYS* 3.3 27.3 - - - +
161B ALA* 4.0 17.2 + - - +
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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
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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