Contacts of the helix formed by residues 115 - 124 (chain H) in PDB entry 2Q9Q
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 115 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14G HIS* 6.5 0.2 - + - -
23H ASP* 4.0 28.4 + - + +
26H LEU* 4.2 13.1 - - + +
27H MET* 3.3 37.9 + - + +
30H GLU* 3.0 27.6 + - - +
113H GLY* 3.4 2.7 - - - -
114H PRO* 1.3 86.4 - - + +
116H PHE* 1.3 54.3 - - - +
117H TYR 3.5 2.0 - - - -
118H GLY* 4.0 4.3 - - - +
119H PHE* 2.8 33.7 + - - +
169H ASP* 3.8 4.3 - - - -
170H GLU* 3.4 32.5 - - + +
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Residues in contact with PHE 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H ILE* 3.9 16.2 - - + -
92H TYR* 2.7 50.1 + + - -
100H PHE* 3.7 34.5 - + - -
109H LEU* 3.8 31.2 - - + -
112H MET 4.8 3.8 - - - -
113H GLY* 4.1 11.1 - - - -
114H PRO 3.4 1.2 - - - -
115H HIS* 1.3 75.7 - - - +
117H TYR* 1.3 71.8 + + - +
120H GLY* 3.1 11.4 + - - -
137H SER* 5.5 2.5 - - - -
138H LEU* 3.6 24.7 - - + +
141H THR* 4.1 23.8 - - + -
169H ASP* 3.2 16.7 + - + +
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Residues in contact with TYR 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E LEU* 3.8 16.6 - - + +
13H LEU* 3.5 21.4 - - + +
109H LEU* 3.6 7.4 - - + +
115H HIS 3.5 0.4 - - - -
116H PHE* 1.3 90.4 - + - +
118H GLY* 1.3 61.4 + - - +
120H GLY 3.9 0.2 - - - -
121H SER* 2.9 31.4 + - - -
138H LEU* 3.3 38.1 - - + +
141H THR* 3.6 10.9 - - + +
142H PHE* 3.4 32.6 + + + -
145H ARG* 3.7 0.7 - - - -
169H ASP* 3.4 29.1 + - - +
171H MET* 4.5 14.4 - - + -
172H GLU* 2.8 34.4 + - + -
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Residues in contact with GLY 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ALA* 3.8 24.3 - - - +
13H LEU* 4.0 7.0 - - - +
27H MET* 4.2 9.4 - - - -
115H HIS* 3.5 7.3 + - - +
116H PHE 3.4 0.4 - - - -
117H TYR* 1.3 76.9 - - - +
119H PHE* 1.3 63.6 + - - +
121H SER 3.5 0.3 + - - -
122H GLN* 3.2 28.8 + - - +
169H ASP* 4.9 0.6 + - - -
171H MET* 6.2 0.4 - - - +
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Residues in contact with PHE 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H MET* 3.7 22.4 - - - -
30H GLU* 3.1 52.5 - - + +
31H LYS 3.9 17.0 - - - -
32H LEU* 4.3 9.9 - - + -
70H LEU* 3.9 27.3 - - + +
89H PRO* 4.1 20.4 - - + -
92H TYR* 3.6 21.3 - + - +
115H HIS* 2.8 22.5 + - - +
118H GLY* 1.3 71.6 - - - -
120H GLY* 1.3 58.7 + - - +
122H GLN* 3.1 4.6 + - - +
123H LEU* 2.8 33.8 + - + +
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Residues in contact with GLY 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H TYR* 3.3 29.7 + - - -
116H PHE 3.1 13.8 + - - -
117H TYR 3.9 0.7 - - - -
119H PHE* 1.3 78.2 - - - +
121H SER* 1.3 60.3 + - - +
123H LEU* 3.2 20.4 + - - +
124H LEU* 3.7 10.0 + - - +
134H ILE* 4.1 4.2 - - - +
138H LEU* 3.6 14.3 - - - +
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Residues in contact with SER 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E LEU* 4.6 2.5 - - - -
173E ASN* 3.7 15.7 - - - +
12H ALA 3.1 24.7 + - - -
13H LEU* 3.3 20.0 + - - -
14H GLY 3.3 8.8 + - - +
15H PRO 5.5 0.2 - - - +
117H TYR 2.9 18.5 + - - -
118H GLY 3.9 0.2 - - - -
120H GLY* 1.3 77.0 - - - +
122H GLN* 1.3 62.2 + - - +
124H LEU* 3.3 27.1 - - - +
125H HIS* 4.7 3.5 + - - -
138H LEU* 3.8 3.7 - - - +
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Residues in contact with GLN 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ALA* 3.0 30.1 + - + +
14H GLY 3.4 16.8 + - - -
15H PRO 3.8 7.0 + - - +
16H GLU* 4.1 0.5 - - - -
17H GLU* 4.0 15.6 + - - +
27H MET* 3.5 25.8 - - + -
70H LEU* 4.4 8.5 - - + -
74H LYS* 3.1 28.6 + - - +
118H GLY 3.2 15.2 + - - +
119H PHE* 3.1 5.2 + - - +
121H SER* 1.3 74.0 - - - +
123H LEU* 1.3 65.4 + - - +
124H LEU 3.0 2.0 - - - -
125H HIS* 3.0 41.4 + - - +
126H PHE* 4.1 5.6 - - - -
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Residues in contact with LEU 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H LEU* 5.2 5.6 - - + -
70H LEU* 5.1 2.0 - - - +
86H VAL* 5.7 1.8 - - + -
87H GLU 5.3 0.7 - - - +
88H LEU* 3.5 35.7 - - + -
89H PRO* 4.0 13.2 - - + -
92H TYR* 3.7 39.5 - - + -
119H PHE* 2.8 21.6 + - + +
120H GLY 3.2 13.0 - - - +
122H GLN* 1.3 78.4 - - - +
124H LEU* 1.3 57.5 + - - +
125H HIS 2.9 6.3 + - - -
126H PHE* 2.9 43.7 + - + +
128H SER* 5.8 1.0 - - - -
131H ASN* 4.6 2.3 - - - +
134H ILE* 4.2 9.2 - - + -
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Residues in contact with LEU 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ASN* 3.5 42.8 - - + +
174E LEU* 4.1 13.2 - - + -
120H GLY 3.7 5.4 - - - +
121H SER* 3.3 22.9 - - - +
122H GLN 3.0 0.4 - - - -
123H LEU* 1.3 76.2 - - - +
125H HIS* 1.3 60.0 + - + +
126H PHE 3.2 2.5 + - - -
127H ASP* 3.7 2.3 + - - -
131H ASN* 3.0 64.3 + - + +
134H ILE* 4.0 19.3 - - + -
135H SER* 4.1 5.6 - - - +
138H LEU* 5.3 0.4 - - + -
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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