Contacts of the helix formed by residues 105 - 114 (chain B) in PDB entry 3H44
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 GLY 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B ASP* 3.1 17.3 + - - -
103B ILE 3.3 0.2 + - - -
104B ALA* 1.3 74.0 - - - +
106B LEU* 1.3 66.1 + - - +
107B SER 3.4 2.5 - - - -
108B HIS* 3.3 5.3 + - - +
109B PHE* 3.0 24.1 + - - +
218B PHE 3.7 2.4 + - - -
219B GLY 3.4 16.8 - - - -
220B THR 4.0 0.4 - - - -
221B GLY* 3.7 13.2 - - - -
226B LEU* 3.7 6.3 - - - +
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Residues in contact with LEU 106 (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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99B ASP* 3.5 8.6 + - - +
100B PRO* 3.7 28.9 - - + -
103B ILE* 3.6 27.8 + - + +
104B ALA 3.5 2.8 - - - -
105B GLY* 1.3 78.1 - - - +
107B SER* 1.3 58.7 + - - +
109B PHE* 3.2 4.0 + - + +
110B LEU* 2.7 29.7 + - + +
226B LEU* 4.0 6.0 - - + +
237B VAL* 4.6 11.9 - - + -
240B GLU* 3.8 30.7 - - + +
241B LEU* 3.7 28.5 - - + +
244B PHE* 4.1 15.3 - - + -
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Residues in contact with SER 107 (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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94B ILE* 5.3 0.2 - - - -
95B GLY* 3.4 10.2 - - - -
96B SER* 3.1 22.0 + - - -
99B ASP* 2.6 28.5 + - - -
106B LEU* 1.3 71.7 - - - +
108B HIS* 1.3 64.4 + - - +
110B LEU* 3.6 8.8 - - - +
111B GLN* 3.0 23.0 + - - +
142B THR* 3.7 9.6 + - - +
147B THR* 4.8 5.9 - - - +
244B PHE* 3.8 25.5 - - - -
249B TYR* 5.1 2.2 + - - -
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Residues in contact with HIS 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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1B ZN 1.8 32.2 - - - -
96B SER* 5.2 0.2 - - - -
105B GLY 3.3 4.6 + - - +
107B SER* 1.3 77.1 + - - +
109B PHE* 1.3 63.1 + - - +
111B GLN* 3.2 12.1 + - - +
112B HIS* 2.6 26.7 + + - -
142B THR* 3.6 15.3 - - + +
186B VAL* 3.9 10.8 - - + +
189B GLU* 2.3 31.3 + - + -
219B GLY 3.9 11.3 + - - +
220B THR* 3.0 37.1 + - + +
18D SER* 3.6 25.9 + - - -
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Residues in contact with PHE 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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105B GLY 3.0 13.3 + - - +
106B LEU* 3.4 10.3 - - + +
108B HIS* 1.3 77.9 + - - +
110B LEU* 1.3 62.4 + - - +
112B HIS* 3.1 4.3 + - + +
113B MET* 3.0 36.8 + - + +
179B LYS* 3.7 38.8 - - + -
182B GLU* 4.0 7.0 - - + -
183B VAL* 3.8 27.4 - - + -
186B VAL* 4.0 18.6 - - + -
220B THR 5.2 0.2 + - - -
226B LEU* 3.6 37.9 - - + -
237B VAL* 4.4 16.2 - - + -
241B LEU* 4.4 15.0 - - + -
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Residues in contact with LEU 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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106B LEU 2.7 18.9 + - - +
107B SER* 3.6 7.0 - - - +
109B PHE* 1.3 71.5 - - - +
111B GLN* 1.3 57.9 + - - +
113B MET* 2.9 20.8 + - - +
114B LEU* 3.0 37.5 + - + +
174B PHE* 4.1 11.4 - - + -
241B LEU* 3.8 33.6 - - + +
244B PHE* 3.3 34.5 - - + -
245B HIS* 4.0 12.3 - - + +
249B TYR* 3.4 33.0 - - + +
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Residues in contact with GLN 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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1B ZN 3.7 7.1 - - - -
107B SER 3.0 8.5 + - - +
108B HIS* 3.2 13.2 - - - +
110B LEU* 1.3 74.9 - - - +
112B HIS* 1.3 63.7 + - - +
114B LEU 3.8 2.9 + - - -
115B PHE* 3.2 19.6 - - - -
140B ALA* 3.7 25.3 - - + +
141B PHE 3.2 3.2 - - - -
142B THR* 2.4 48.9 + - - +
147B THR* 4.1 4.9 - - + -
149B TYR* 3.3 26.5 - - + +
18D SER 3.3 10.3 + - - -
20D GLN* 3.2 32.7 - - - +
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Residues in contact with HIS 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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1B ZN 2.1 14.6 - - - -
108B HIS* 3.0 32.8 + + - -
109B PHE* 3.1 9.4 + - + +
111B GLN* 1.3 81.1 - - - +
113B MET* 1.3 62.3 + - - +
115B PHE* 3.5 19.1 + - - +
116B LEU* 4.1 6.8 - - - +
182B GLU* 3.1 36.1 + - + +
185B ALA* 4.4 2.4 - - + +
186B VAL* 3.9 18.1 - - + +
189B GLU* 1.9 38.5 + - + -
824B ARG* 3.5 19.5 + - - -
20D GLN* 3.3 18.2 + - + +
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Residues in contact with MET 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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109B PHE* 3.0 33.8 + - + +
110B LEU 2.9 9.7 + - - +
112B HIS* 1.3 71.9 - - - +
114B LEU* 1.3 56.8 + - - +
115B PHE 2.9 6.3 - - - -
116B LEU* 2.8 51.3 + - + +
117B GLY 4.4 1.7 + - - +
172B PRO* 5.7 0.3 - - - +
174B PHE* 3.7 45.1 + - + -
175B ASP 4.0 6.7 - - - +
178B ALA* 4.3 3.1 - - + -
179B LYS* 3.9 34.5 - - + +
182B GLU* 4.1 3.6 - - - -
241B LEU* 4.1 15.5 - - + -
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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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110B LEU* 3.0 25.4 + - + +
111B GLN 4.3 0.7 - - - +
112B HIS 3.5 0.8 - - - -
113B MET* 1.3 75.0 - - - +
115B PHE* 1.3 59.0 + - - +
117B GLY 4.4 4.8 + - - +
118B THR* 4.7 4.7 - - - +
149B TYR* 3.6 30.7 - - + +
168B PHE* 3.4 60.4 - - + +
169B PHE* 4.8 1.6 - - + -
172B PRO* 3.7 22.0 - - + -
174B PHE* 3.5 31.2 - - + -
245B HIS* 3.9 2.5 - - + -
249B TYR* 3.9 18.4 - - + -
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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