Contacts of the helix formed by residues 110 - 122 (chain A) in PDB entry 2HJ8
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 THR 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A THR 3.8 4.5 + - - +
109A GLN* 1.3 84.1 - - - +
111A VAL* 1.3 65.2 - - - +
112A ALA* 3.7 4.9 + - - +
113A HIS* 3.0 41.9 + - + +
114A LEU 3.1 8.8 + - - -
140A ASP 3.8 8.7 - - - +
141A GLN 4.2 9.0 - - - +
142A LEU 3.5 21.1 - - - +
143A PRO* 3.7 12.8 - - + -
144A LEU* 4.0 2.0 - - - -
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Residues in contact with VAL 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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110A THR* 1.3 73.7 - - - +
112A ALA* 1.3 56.5 + - - +
114A LEU* 3.2 12.4 + - + +
115A LYS* 2.9 27.4 + - - +
130A TRP* 4.9 13.8 - - + -
131A LEU* 5.5 5.2 - - + +
137A PRO 5.0 0.2 - - - +
138A LEU* 4.6 18.8 - - + -
139A GLU 3.7 20.4 - - - +
140A ASP* 3.7 15.9 + - + -
142A LEU 3.4 5.9 + - - +
144A LEU* 3.6 36.3 - - + +
147A TYR* 4.5 11.4 - - + -
155A VAL* 6.4 1.3 - - + -
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Residues in contact with ALA 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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110A THR* 3.1 6.9 - - - +
111A VAL* 1.3 79.4 - - - +
113A HIS* 1.3 59.7 + - + +
115A LYS* 3.3 17.2 + - - +
116A GLN* 2.9 27.0 + - - +
140A ASP* 3.3 37.4 + - + +
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Residues in contact with HIS 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 GLN* 3.4 30.7 + - + +
110A THR* 3.0 25.6 + - + +
112A ALA* 1.3 78.3 - - + +
114A LEU* 1.3 60.2 + - - +
116A GLN* 3.2 25.7 + - - +
117A GLN* 2.9 26.5 + - - +
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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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91A ILE* 4.5 13.7 - - + -
93A VAL* 5.2 3.6 - - + -
103A TYR* 5.1 8.1 - - + -
105A VAL* 3.7 24.5 - - + -
109A GLN* 3.6 13.4 + - - +
110A THR 3.1 5.7 + - - -
111A VAL* 3.3 16.8 - - + +
113A HIS* 1.3 74.3 - - - +
115A LYS* 1.3 64.7 + - - +
117A GLN* 3.2 28.6 + - - +
118A VAL* 3.2 22.0 + - + +
131A LEU* 4.3 23.8 - - + -
144A LEU* 3.7 25.8 - - + -
155A VAL* 4.8 10.1 - - + -
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Residues in contact with LYS 115 (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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111A VAL 2.9 13.5 + - - +
112A ALA* 3.4 18.5 - - - +
114A LEU* 1.3 76.2 - - - +
116A GLN* 1.3 52.8 + - - +
118A VAL* 3.2 9.3 + - - +
119A SER* 2.7 40.7 + - - +
126A ASP* 2.7 41.6 + - + +
129A PHE* 3.9 15.8 - - + -
130A TRP* 4.1 31.4 - - + -
131A LEU* 5.0 5.8 - - + -
140A ASP* 5.3 7.5 + - + +
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Residues in contact with GLN 116 (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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112A ALA 2.9 14.3 + - - +
113A HIS* 3.2 36.5 + - - +
115A LYS* 1.3 76.2 - - - +
117A GLN* 1.3 61.1 + - - +
119A SER* 3.2 12.9 - - - -
120A GLY* 3.0 23.4 + - - -
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Residues in contact with GLN 117 (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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103A TYR* 3.3 33.1 - - + +
104A GLU 4.5 13.1 + - - +
105A VAL* 5.4 0.9 - - - +
109A GLN* 4.5 14.3 - - - +
113A HIS 2.9 12.2 + - - +
114A LEU* 3.2 21.4 + - - +
116A GLN* 1.3 76.5 - - - +
118A VAL* 1.3 58.0 + - + +
120A GLY* 2.9 17.7 + - - -
121A LEU* 3.3 22.2 + - + +
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Residues in contact with VAL 118 (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 VAL* 6.2 0.2 - - + -
103A TYR* 5.4 14.1 - - + +
114A LEU* 3.3 19.1 - - + +
115A LYS 3.2 6.5 + - - +
117A GLN* 1.3 77.2 - - + +
119A SER* 1.3 56.9 + - - +
121A LEU* 4.5 5.8 - - + +
122A GLU* 2.6 48.5 + - + +
123A GLY 2.8 3.6 + - - -
129A PHE* 3.5 25.8 - - + -
131A LEU* 4.2 26.5 - - + -
157A MET* 4.2 12.6 - - + -
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Residues in contact with SER 119 (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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115A LYS* 2.7 32.8 + - - +
116A GLN* 3.2 20.6 - - - -
117A GLN 3.1 0.4 - - - -
118A VAL* 1.3 73.8 - - - +
120A GLY* 1.3 58.7 + - - +
123A GLY* 3.0 27.2 + - - +
126A ASP* 4.4 7.1 - - - +
129A PHE* 3.3 13.7 - - - -
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Residues in contact with GLY 120 (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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116A GLN 3.0 8.2 + - - -
117A GLN* 2.9 10.1 + - - -
119A SER* 1.3 79.8 - - - +
121A LEU* 1.3 64.6 + - - +
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Residues in contact with LEU 121 (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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103A TYR* 5.4 13.2 - - + +
117A GLN* 3.3 19.2 + - + +
118A VAL* 3.1 7.6 + - + +
120A GLY* 1.3 82.3 - - - +
122A GLU* 1.3 64.0 + - + +
123A GLY 3.3 4.9 + - - -
124A VAL* 5.7 0.9 - - - +
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Residues in contact with GLU 122 (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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118A VAL* 2.6 27.5 + - + +
121A LEU* 1.3 76.8 - - + +
123A GLY* 1.3 48.3 + - - -
124A VAL* 2.5 42.6 + - + +
129A PHE* 3.6 11.5 - - + +
157A MET* 3.8 22.4 - - + -
159A LEU* 5.6 2.7 - - + -
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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