Contacts of the helix formed by residues 94 - 105 (chain A) in PDB entry 3H0G
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 HIS 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PHE* 1.3 81.6 + - - +
95A ILE* 1.3 59.6 + - - +
96A GLY* 4.9 3.6 - - - -
97A PHE* 2.8 59.6 + + + -
98A LEU* 2.3 45.5 + - + +
240A MET 3.8 19.7 - - - +
242A ILE* 3.6 28.5 - - + +
306A VAL* 5.2 5.3 + - - +
307A ALA* 6.3 0.4 - - - -
310A MET* 3.6 37.1 - - + +
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Residues in contact with ILE 95 (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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93A PHE* 5.1 0.9 - - + +
94A HIS* 1.3 77.9 + - - +
96A GLY* 1.3 73.9 + - - +
98A LEU* 2.4 25.4 + - + +
99A SER* 2.9 4.9 + - - -
102A LYS* 6.2 1.6 - - - +
187A LEU* 4.8 18.8 - - + -
303A GLN 5.2 2.7 - - - +
306A VAL 5.9 0.2 + - - -
307A ALA* 3.3 28.8 - - + +
310A MET* 5.5 5.7 - - + +
311A ASP* 4.1 8.3 - - + +
314A ILE* 2.5 68.6 - - + -
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Residues in contact with GLY 96 (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 HIS* 3.4 4.1 + - - -
95A ILE* 1.3 89.4 - - - +
97A PHE* 1.3 55.5 + - - +
98A LEU 2.5 7.6 + - - -
99A SER* 2.7 26.1 + - - -
310A MET* 6.0 2.0 - - - +
311A ASP* 4.9 6.5 + - - -
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Residues in contact with PHE 97 (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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23A ILE* 4.2 38.4 - - + -
94A HIS* 2.8 42.0 - + + -
95A ILE 3.6 0.2 - - - -
96A GLY* 1.3 69.8 - - - +
98A LEU* 1.3 60.6 + - - +
99A SER 3.3 0.2 - - - -
100A LYS* 3.4 14.0 + - + +
101A ILE* 3.2 21.7 + - - +
240A MET* 3.9 31.9 - - + +
310A MET* 6.3 0.2 - - + -
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Residues in contact with LEU 98 (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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93A PHE* 3.3 36.8 - - + -
94A HIS* 2.3 61.3 + - + +
95A ILE* 2.4 41.1 + - + +
97A PHE* 1.3 66.0 - - - +
99A SER* 1.3 62.3 + - - +
101A ILE* 2.5 39.0 - - + +
102A LYS* 3.0 30.2 + - - +
240A MET* 5.3 4.0 - - + +
241A ILE* 6.0 5.4 - - + -
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Residues in contact with SER 99 (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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95A ILE* 2.9 5.0 + - - -
96A GLY* 2.7 23.0 + - - -
98A LEU* 1.3 72.7 - - - +
100A LYS* 1.3 71.1 + - - +
102A LYS* 3.2 13.1 + - - +
103A LYS* 3.1 36.1 + - - +
184A LYS* 5.8 5.8 - - - -
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Residues in contact with LYS 100 (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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97A PHE* 3.4 16.1 + - + +
98A LEU 3.2 1.0 - - - -
99A SER* 1.3 82.1 + - - +
101A ILE* 1.3 67.7 + - - +
103A LYS* 2.8 24.9 + - + +
104A ILE* 3.1 26.2 + - + +
137A LEU* 4.9 23.9 - - + +
229A GLY 4.6 13.3 + - - -
230A LEU* 4.6 13.3 - - - +
240A MET* 4.7 12.1 - - + -
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Residues in contact with ILE 101 (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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97A PHE 3.2 3.0 + - - +
98A LEU* 2.5 51.4 - - + +
100A LYS* 1.3 78.8 - - - +
102A LYS* 1.3 67.0 + - + +
104A ILE* 3.6 19.5 - - + +
105A LEU* 3.7 9.0 + - - +
213A VAL* 4.3 7.4 - - + -
217A PHE* 2.7 48.5 - - + -
240A MET* 3.2 41.2 - - + -
241A ILE* 5.8 2.7 - - + -
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Residues in contact with LYS 102 (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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93A PHE* 5.6 3.6 - - - -
95A ILE* 6.2 1.6 - - - +
98A LEU* 3.0 45.2 + - + +
99A SER* 3.4 11.8 - - - +
101A ILE* 1.3 81.8 - - + +
103A LYS* 1.3 62.2 + - + +
105A LEU* 2.9 36.9 - - + +
184A LYS* 4.8 25.0 - - + +
186A GLY 5.1 0.6 + - - -
187A LEU* 5.0 17.0 + - - +
188A ARG 5.3 0.4 - - - +
189A LEU* 3.8 46.5 - - + +
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Residues in contact with LYS 103 (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 SER* 3.1 26.6 + - - +
100A LYS* 2.8 13.7 + - + +
102A LYS* 1.3 75.7 - - + +
104A ILE* 1.3 69.6 + - - +
105A LEU* 4.0 3.3 - - - +
141A TRP* 4.4 26.2 - - + +
144A CYS* 5.2 1.2 - - - +
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Residues in contact with ILE 104 (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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100A LYS* 3.1 29.1 + - + +
101A ILE* 3.6 13.7 - - + +
103A LYS* 1.3 78.5 - - - +
105A LEU* 1.3 77.1 + - - +
106A GLU 3.0 0.9 + - - -
107A CYS* 3.2 42.1 - - + +
108A VAL* 6.2 0.2 - - + -
137A LEU* 6.0 6.3 - - + -
140A VAL* 4.7 0.6 - - - +
141A TRP* 5.8 0.2 - - - -
144A CYS* 3.4 12.3 - - - -
217A PHE* 5.4 12.3 - - + -
228A LEU* 6.3 2.2 - - + -
230A LEU* 5.6 5.6 - - + -
237A PRO* 5.5 6.1 - - + -
240A MET* 4.0 28.0 - - + -
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Residues in contact with LEU 105 (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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101A ILE 3.7 7.6 + - - +
102A LYS* 2.9 33.4 - - + +
103A LYS 4.0 2.5 - - - +
104A ILE* 1.3 87.5 - - - +
106A GLU* 1.3 82.6 + - - +
110A TRP* 5.8 9.0 - - + -
144A CYS* 3.3 2.3 - - - +
182A ILE* 3.0 49.1 - - + -
189A LEU* 5.2 10.1 - - + -
208A LEU* 6.4 2.0 - - + -
213A VAL* 6.0 7.9 - - + -
217A PHE* 6.4 1.8 - - + -
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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