Contacts of the helix formed by residues 107 - 116 (chain B) in PDB entry 3T0E
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 TYR 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.3 7.8 - - + +
9A GLN* 3.3 40.7 + - - +
24A PHE* 3.5 7.1 - - - -
4B GLY 6.4 0.7 - - - -
5B ALA* 4.0 5.2 - - - -
6B GLU* 2.9 58.6 - - + +
42B HIS* 4.0 9.6 + - + +
43B GLU 4.1 2.0 - - - -
44B CYS* 3.2 31.2 - - - -
55B PHE* 4.5 6.3 - + + -
103B ALA* 2.7 22.1 + - - +
106B THR* 1.3 72.4 + - - +
108B CYS* 1.3 80.8 + - - +
110B HIS* 3.4 3.5 + - - +
111B ASN* 3.0 47.7 + - - +
29C THR* 5.5 0.9 - - - -
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Residues in contact with CYS 108 (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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7A ILE* 6.1 0.2 - - - -
44B CYS* 2.0 55.4 - - - -
46B PHE* 3.6 18.1 - - + -
53B VAL* 4.2 9.6 - - + -
55B PHE* 4.0 18.6 - - - -
103B ALA 3.6 0.8 + - - -
104B VAL* 3.4 16.1 + - - +
107B TYR* 1.3 83.3 - - - +
109B ARG* 1.3 68.9 + - - +
110B HIS 3.0 0.5 + - - -
111B ASN* 3.9 1.8 - - - +
112B TYR* 2.9 24.6 + - - +
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Residues in contact with ARG 109 (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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46B PHE* 4.6 3.1 - - + -
50B THR* 3.1 51.3 + - + +
51B GLU 3.8 5.3 + - - -
52B ARG* 4.9 1.2 - - - +
53B VAL* 3.6 26.9 - - + +
104B VAL* 2.8 51.0 + - - +
105B ASP* 2.9 33.4 + - - +
108B CYS* 1.3 72.4 - - - +
110B HIS* 1.3 58.3 + - - +
112B TYR* 3.6 7.1 - - - +
113B GLY* 2.8 27.2 + - - -
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Residues in contact with HIS 110 (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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1B PHE 4.8 3.1 - - - -
2B SER 2.9 23.3 + - - -
4B GLY 3.8 4.2 + - - -
105B ASP 4.1 5.4 + - - +
106B THR 3.2 21.5 - - - +
107B TYR 3.4 1.7 + - - +
108B CYS 3.0 1.8 + - - -
109B ARG* 1.3 74.3 - - - +
111B ASN* 1.3 74.5 + - - +
113B GLY* 2.6 25.6 + - - -
114B VAL* 3.1 21.4 + - + +
27C SER* 3.6 5.8 + - - -
28C GLY* 3.6 36.2 - - - -
29C THR* 3.1 23.3 - - + +
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Residues in contact with ASN 111 (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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7A ILE* 4.2 11.6 - - + +
24A PHE* 4.1 3.6 - - - -
3B TRP* 3.3 30.4 + - + +
4B GLY 2.7 44.2 + - - +
107B TYR* 3.0 48.8 + - - +
108B CYS* 4.0 2.0 - - - +
110B HIS* 1.3 80.7 - - - +
112B TYR* 1.3 64.6 + - - +
114B VAL* 2.9 18.9 + - - +
115B GLY* 3.1 10.6 + - - -
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Residues in contact with TYR 112 (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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5A HIS* 4.5 14.1 - + + -
7A ILE* 4.1 13.8 - - + +
26A PHE* 5.8 2.9 - + - -
46B PHE* 3.3 46.7 - + + -
49B GLY* 3.8 21.4 + - - -
50B THR* 4.6 13.2 - - - -
108B CYS 2.9 18.3 + - - +
109B ARG* 3.6 5.4 - - - +
111B ASN* 1.3 77.1 - - - +
113B GLY* 1.3 57.7 + - - +
115B GLY* 3.2 3.0 + - - +
116B GLU* 2.8 61.6 + - + +
120B VAL* 3.6 35.3 - - + +
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Residues in contact with GLY 113 (chain B).
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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109B ARG 2.8 11.3 + - - -
110B HIS* 2.6 16.7 + - - -
112B TYR* 1.3 77.6 - - - +
114B VAL* 1.3 60.4 + - - +
116B GLU* 3.9 18.9 + - - +
117B SER 5.3 0.2 + - - -
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Residues in contact with VAL 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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51A PHE* 4.6 5.2 - - + +
52A ALA* 4.0 20.9 - - + +
1B PHE* 4.0 22.0 - - - +
2B SER 4.2 2.9 - - - +
3B TRP* 3.6 28.3 - - + -
110B HIS* 3.1 27.1 + - + +
111B ASN* 2.9 10.0 + - - +
113B GLY* 1.3 80.0 - - - +
115B GLY* 1.3 57.3 + - - +
116B GLU 3.3 0.8 + - - -
117B SER* 3.5 16.5 + - - -
118B PHE* 3.6 9.9 - - + -
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Residues in contact with GLY 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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3B TRP* 4.4 4.5 - - - -
111B ASN 3.1 9.3 + - - -
112B TYR* 3.5 3.8 - - - -
114B VAL* 1.3 77.5 - - - +
116B GLU* 1.3 57.0 + - - +
117B SER* 2.8 13.6 + - - -
118B PHE* 4.0 20.2 - - - -
119B THR* 3.2 36.5 + - - -
120B VAL* 3.5 2.2 + - - -
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Residues in contact with GLU 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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49B GLY* 5.8 0.5 - - - -
50B THR* 4.5 7.3 + - - -
112B TYR* 2.8 44.1 + - + +
113B GLY* 3.9 15.2 - - - +
114B VAL 3.3 1.2 - - - -
115B GLY* 1.3 77.1 - - - +
117B SER* 1.3 56.0 + - - +
120B VAL* 3.8 14.4 - - + +
121B GLN* 2.9 39.0 + - - +
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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