Contacts of the helix formed by residues 110 - 117 (chain B) in PDB entry 2G43
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 SER 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ALA 4.3 6.5 + - - -
20B PHE* 5.5 1.9 - - - -
108B ASP* 3.0 13.8 + - - -
109B PRO* 1.3 79.3 + - - +
111B LEU* 1.3 64.2 + - - +
112B ALA* 3.2 3.8 - - - -
113B GLU* 3.0 22.0 + - - +
114B HIS* 3.0 34.2 + - - -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 4.4 15.5 - - + -
85B VAL* 5.0 2.9 - - + -
94B GLY* 4.4 2.2 - - - -
95B ALA* 3.8 32.8 - - + +
97B VAL* 4.1 18.4 - - + -
108B ASP* 2.9 31.3 + - + +
109B PRO 3.4 1.8 - - - -
110B SER* 1.3 75.8 - - - +
112B ALA* 1.3 65.2 + - - +
114B HIS* 3.1 2.3 + - + +
115B LEU* 2.9 48.1 + - + +
122B MET* 4.0 21.1 - - + -
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B PRO 5.1 2.1 + - - +
110B SER* 3.2 1.5 - - - -
111B LEU* 1.3 77.8 - - - +
113B GLU* 1.3 60.2 + - - +
115B LEU* 3.6 1.6 + - - +
116B SER* 2.9 29.7 + - - -
120B ILE 5.1 0.5 - - - +
122B MET* 3.8 26.5 - - + +
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLN* 4.4 3.3 - - - +
110B SER* 3.0 25.2 + - - +
112B ALA* 1.3 75.8 - - - +
114B HIS* 1.3 78.3 + - + +
116B SER* 3.2 17.4 + - - -
117B HIS* 3.3 10.9 + - - +
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Residues in contact with HIS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ALA* 3.4 26.5 + - - -
20B PHE 5.6 1.6 + - - -
22B LEU* 3.6 39.4 + - + +
24B GLN* 3.0 39.8 + - + +
51B LEU* 4.4 13.9 - - + +
83B LEU* 5.4 0.4 - - + -
108B ASP* 2.7 30.7 + - - +
110B SER* 3.0 15.0 + - - -
111B LEU* 3.1 8.0 + - - +
113B GLU* 1.3 88.1 + - + +
115B LEU* 1.3 61.6 + - - +
117B HIS* 3.2 9.0 - - - +
118B PHE* 3.4 7.0 - - - -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 4.1 8.3 - - + -
51B LEU* 3.9 22.9 - - + -
85B VAL* 4.2 7.0 - - + -
90B ILE* 4.1 19.3 - - + -
111B LEU* 2.9 39.4 + - + +
112B ALA* 4.1 3.1 - - - +
114B HIS* 1.3 71.9 - - - +
116B SER* 1.3 61.4 + - - +
117B HIS 3.0 2.2 - - - -
118B PHE* 2.8 21.8 + - + +
119B GLY 3.4 0.2 + - - -
120B ILE* 3.2 48.8 + - + +
122B MET* 3.7 29.8 - - + -
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA 2.9 19.2 + - - -
113B GLU* 3.2 12.4 + - - -
115B LEU* 1.3 76.6 - - - +
117B HIS* 1.3 57.4 + - - +
119B GLY* 2.7 23.2 + - - +
120B ILE 3.9 13.7 + - - +
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Residues in contact with HIS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLN* 3.3 44.5 + - + +
25B LEU 2.7 30.9 + - - -
26B ASP* 5.0 1.8 - - - -
28B PRO* 3.2 57.8 - - + +
52B THR 5.1 0.4 - - - -
113B GLU 3.3 5.2 + - - +
114B HIS 3.2 17.0 - - - +
116B SER* 1.3 78.0 - - - +
118B PHE* 1.3 66.8 + + - +
119B GLY 3.7 0.5 + - - -
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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