Contacts of the helix formed by residues 110 - 119 (chain A) in PDB entry 2M8N
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 5.6 0.9 - - - +
109A SER* 1.3 77.5 - - - +
111A LEU* 1.3 65.7 + - - +
112A GLN* 3.7 9.1 + - - +
113A GLU* 3.1 37.3 + - - +
114A GLN* 2.9 26.9 + - - +
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Residues in contact with LEU 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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12A HIS* 3.1 58.1 - - + +
48A THR* 3.7 28.5 - - + +
50A GLN* 3.2 37.4 + - - +
51A ASP* 5.6 2.0 - - - +
110A THR* 1.3 72.9 - - - +
112A GLN* 1.3 63.4 + - - +
114A GLN* 3.0 13.1 + - - +
115A ILE* 2.8 29.4 + - + +
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Residues in contact with GLN 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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9A GLN* 4.1 21.5 + - - +
10A MET 5.1 3.1 + - - +
12A HIS* 4.8 14.4 + - + -
110A THR* 3.1 9.1 + - - +
111A LEU* 1.3 80.3 - - - +
113A GLU* 1.3 57.5 + - + +
115A ILE* 3.4 13.7 + - - +
116A GLY* 2.9 29.3 + - - +
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Residues in contact with GLU 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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103A ASP* 5.2 0.5 - - - +
108A THR 4.3 2.9 - - - +
109A SER* 3.5 14.9 + - - -
110A THR* 3.1 38.3 + - - +
112A GLN* 1.3 75.1 - - + +
114A GLN* 1.3 66.9 + - - +
116A GLY* 3.3 2.7 + - - -
117A TRP* 2.9 48.0 + - + -
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Residues in contact with GLN 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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2A ILE* 5.5 0.4 - - - -
48A THR* 3.7 12.9 + - - -
49A PRO* 3.4 42.6 - - + +
50A GLN* 3.2 30.0 + - - +
103A ASP 4.3 2.6 + - - +
106A GLY* 3.6 19.6 + - - -
109A SER* 3.9 22.2 + - - -
110A THR 2.9 16.2 + - - +
111A LEU* 3.0 13.1 + - - +
113A GLU* 1.3 74.4 - - - +
115A ILE* 1.3 58.7 + - - +
117A TRP* 3.2 5.6 + - + +
118A MET* 2.9 30.3 + - - +
126A VAL* 3.9 11.9 - - + +
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Residues in contact with ILE 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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1A PRO 5.1 0.2 - - - +
2A ILE* 4.0 27.8 - - + -
10A MET* 3.7 34.5 - - + +
11A VAL* 3.8 5.2 - - - +
12A HIS* 3.3 53.8 - - + +
48A THR* 4.5 7.6 - - + -
111A LEU* 2.8 20.2 + - + +
112A GLN* 3.8 12.8 - - - +
114A GLN* 1.3 75.4 - - - +
116A GLY* 1.3 63.5 + - - +
119A THR* 2.8 32.0 + - + +
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Residues in contact with GLY 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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96A MET* 5.3 15.4 - - - +
112A GLN* 2.9 19.5 + - - +
113A GLU* 3.3 4.7 + - - -
115A ILE* 1.3 76.6 - - - +
117A TRP* 1.3 63.4 + - - +
119A THR* 4.0 4.6 + - - -
120A HIS* 3.5 20.6 + - - +
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Residues in contact with TRP 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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96A MET* 3.9 18.4 + - + +
97A ARG* 2.7 29.4 + - + -
98A GLU* 3.5 3.1 - - - +
99A PRO* 3.2 41.9 - - + +
103A ASP* 3.4 25.1 - - + -
109A SER* 3.5 24.5 - - - -
113A GLU* 2.9 41.0 + - + +
114A GLN* 3.7 7.6 - - + +
115A ILE 3.2 0.2 - - - -
116A GLY* 1.3 78.3 - - - +
118A MET* 1.3 60.1 + - - +
120A HIS* 3.2 12.3 + - + +
124A ILE* 2.8 64.2 + - + +
126A VAL* 4.0 10.5 - - + -
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Residues in contact with MET 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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2A ILE* 3.7 28.9 - - + -
46A GLY* 5.6 13.2 - - - +
47A ALA 5.9 1.3 - - - +
48A THR* 5.8 2.7 - - + -
114A GLN 2.9 16.9 + - - +
115A ILE 3.5 0.9 + - - +
117A TRP* 1.3 78.0 - - - +
119A THR* 1.3 56.5 + - + +
123A PRO* 3.2 25.8 - - + +
124A ILE 3.3 6.4 + - - +
125A PRO* 3.7 32.3 - - + -
126A VAL* 4.4 4.5 - - + -
127A GLY* 4.4 9.4 - - - +
128A GLU* 5.0 7.0 - - + +
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Residues in contact with THR 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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2A ILE* 4.1 19.5 - - + -
10A MET* 3.6 35.1 - - + +
115A ILE* 2.8 24.5 + - - +
116A GLY* 4.0 5.1 + - - -
118A MET* 1.3 78.2 - - + +
120A HIS* 1.3 66.8 + - - +
121A ASN* 3.9 0.9 + - - +
123A PRO* 5.4 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