Contacts of the helix formed by residues 105 - 114 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ASP* 2.6 20.9 + - - -
104A ALA* 1.3 73.2 - - - +
106A LEU* 1.3 58.2 + - - +
107A SER 3.3 2.5 - - - -
108A HIS* 3.3 5.1 + - - +
109A PHE* 2.8 29.8 + - - +
218A PHE 3.6 1.8 + - - -
219A GLY 3.2 21.1 - - - -
220A THR 3.9 10.7 - - - +
221A GLY* 4.1 1.3 - - - -
226A LEU* 3.9 4.2 - - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASP* 3.4 3.4 + - - -
100A PRO* 3.7 27.4 - - + -
103A ILE* 3.5 22.1 + - + +
104A ALA 3.5 2.6 + - - -
105A GLY* 1.3 77.0 - - - +
107A SER* 1.3 52.0 + - - +
109A PHE* 3.2 2.5 + - + +
110A LEU* 2.6 36.1 + - + +
226A LEU* 4.1 13.2 - - + -
237A VAL* 4.5 13.5 - - + -
240A GLU* 3.8 18.4 - - + +
241A LEU* 3.8 35.0 - - + +
244A PHE* 3.6 34.3 - - + -
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE* 5.4 0.7 - - - -
95A GLY* 3.3 9.3 - - - -
96A SER* 3.3 21.7 + - - -
99A ASP* 3.0 19.4 + - - -
106A LEU* 1.3 74.8 - - - +
108A HIS* 1.3 60.5 + - - +
110A LEU* 3.6 8.5 - - - +
111A GLN* 2.9 28.1 + - - +
142A THR* 3.6 11.0 + - - +
147A THR* 4.8 4.6 + - - -
244A PHE* 3.6 29.0 - - - -
249A TYR* 4.9 3.4 + - - -
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Residues in contact with HIS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLY* 3.3 5.5 + - - +
107A SER* 1.3 75.4 + - - +
109A PHE* 1.3 66.0 + - - +
111A GLN* 3.1 14.7 + - - +
112A HIS* 2.6 25.5 + + - -
142A THR* 3.5 15.1 - - + +
186A VAL* 3.6 19.7 - - + +
189A GLU* 2.3 26.8 + - - -
219A GLY 3.6 19.0 + - - +
220A THR* 3.0 24.6 + - + -
18C SER* 3.6 16.7 - - - -
42C ZN 1.9 34.5 - - - -
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Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLY 2.8 20.2 + - - +
106A LEU* 3.5 5.2 - - + +
108A HIS* 1.3 70.1 + - - +
110A LEU* 1.3 67.6 + - - +
112A HIS* 3.0 6.5 + - + -
113A MET* 2.9 42.1 + - + +
179A LYS* 3.5 40.6 - - + -
182A GLU* 4.0 6.5 - - + -
183A VAL* 3.7 34.8 - - + -
186A VAL* 4.1 17.7 - - + -
220A THR 5.3 0.2 + - - -
226A LEU* 3.7 31.4 - - + -
237A VAL* 4.4 8.5 - - + -
241A LEU* 4.3 17.9 - - + -
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU 2.6 21.1 + - - +
107A SER* 3.6 9.0 - - - +
109A PHE* 1.3 70.9 - - - +
111A GLN* 1.3 61.8 + - - +
113A MET* 3.1 3.4 + - - +
114A LEU* 3.1 41.1 + - + +
174A PHE* 4.0 6.3 - - + -
241A LEU* 3.5 41.4 - - + +
244A PHE* 3.7 28.5 - - + -
245A HIS* 3.9 15.0 - - + +
249A TYR* 3.5 32.5 - - + +
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Residues in contact with GLN 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A SER 2.9 13.8 + - - +
108A HIS* 3.4 21.1 - - - +
109A PHE 3.0 0.4 - - - -
110A LEU* 1.3 79.2 - - - +
112A HIS* 1.3 69.6 + - - +
114A LEU 3.6 3.5 + - - -
115A PHE* 3.4 16.1 - - - -
140A ALA* 3.5 34.2 - - + +
141A PHE 3.5 0.6 - - - +
142A THR* 2.7 30.9 + - - +
147A THR* 3.9 6.3 - - + -
149A TYR* 3.2 27.8 - - + +
18C SER 3.5 13.3 + - - -
20C GLN* 3.1 26.2 - - - +
42C ZN 4.0 0.9 - - - -
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Residues in contact with HIS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A HIS* 2.6 31.0 + + - +
109A PHE* 3.0 8.7 + - + +
111A GLN* 1.3 83.2 - - - +
113A MET* 1.3 61.1 + - - +
114A LEU 3.4 0.3 + - - -
115A PHE* 3.5 17.5 + - - +
116A LEU* 4.0 7.3 - - - +
182A GLU* 3.0 37.0 + - + +
185A ALA* 4.6 0.8 - - + +
186A VAL* 3.9 20.8 - - + +
189A GLU* 2.1 17.4 + - + -
824A ARG* 4.1 16.3 + - - -
831A TYR* 4.2 6.1 - + - -
19C ARG 3.3 4.7 - - - -
20C GLN* 3.8 11.0 + - + +
42C ZN 2.0 32.7 - - - -
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Residues in contact with MET 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 2.9 39.4 + - + +
110A LEU 3.1 7.6 + - - +
112A HIS* 1.3 75.6 - - - +
114A LEU* 1.3 62.8 + - - +
116A LEU* 2.9 39.9 + - + +
117A GLY 4.4 2.1 + - - +
172A PRO* 5.3 1.2 - - - +
174A PHE* 3.7 45.5 + - + -
175A ASP 4.0 1.1 - - - +
178A ALA* 3.9 11.9 - - + -
179A LYS* 3.5 39.3 - - + +
182A GLU* 4.0 4.0 - - - -
241A LEU* 4.2 13.5 - - + -
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 3.1 32.6 + - + +
111A GLN 4.1 5.6 - - - +
112A HIS 3.4 1.0 + - - -
113A MET* 1.3 76.0 - - - +
115A PHE* 1.3 59.6 + - - +
116A LEU 3.3 0.6 + - - -
117A GLY 4.0 5.5 + - - +
118A THR* 4.5 6.4 - - - +
149A TYR* 3.8 21.5 - - + +
168A PHE* 3.1 60.4 - - + +
169A PHE* 4.2 2.5 - - + -
172A PRO* 3.5 35.7 - - + -
174A PHE* 3.8 8.3 - - + -
245A HIS* 4.1 1.8 - - + +
249A TYR* 4.0 17.5 - - + -
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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
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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