Contacts of the helix formed by residues 105 - 118 (chain B) in PDB entry 2CX9
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 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B ALA 3.8 1.2 + - - -
104B GLY* 1.3 77.9 - - - +
106B GLU* 1.3 65.8 + - - +
107B ALA* 3.5 9.2 + - - +
108B GLN* 2.9 34.6 + - - +
109B LYS* 3.0 18.7 + - - +
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Residues in contact with GLU 106 (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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61B TYR* 2.4 36.8 + - - +
104B GLY 4.9 0.3 - - - +
105B SER* 1.3 73.6 - - - +
107B ALA* 1.3 61.4 + - - +
109B LYS* 3.2 23.5 + - - +
110B GLU* 3.0 25.3 + - - +
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Residues in contact with ALA 107 (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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105B SER* 3.1 9.3 + - - +
106B GLU* 1.3 80.1 - - - +
108B GLN* 1.3 64.0 + - + +
110B GLU* 3.5 5.3 + - - +
111B ALA* 3.1 22.5 + - - +
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Residues in contact with GLN 108 (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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100B ILE* 4.6 2.9 - - + -
103B ALA 4.2 1.2 - - - +
104B GLY* 3.3 12.2 - - - -
105B SER* 2.9 39.3 + - - +
107B ALA* 1.3 74.8 - - + +
109B LYS* 1.3 66.0 + - - +
111B ALA* 3.1 3.3 + - - -
112B PHE* 2.9 46.2 + - + +
191B ALA* 5.7 1.2 - - - +
228B GLU* 2.9 28.5 + - + +
229B ALA 4.1 2.2 + - - -
230B LEU 2.7 31.7 + - - +
231B LEU* 3.6 14.9 - - + +
232B GLY 4.9 0.7 + - - -
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Residues in contact with LYS 109 (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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61B TYR* 3.6 36.5 - - + +
100B ILE* 4.0 13.2 - - - +
101B LEU* 3.6 26.1 + - + +
102B LEU 5.5 1.1 + - - -
104B GLY 3.1 23.1 + - - +
105B SER 3.0 15.7 + - - +
106B GLU* 3.2 22.9 + - - +
108B GLN* 1.3 76.9 - - - +
110B GLU* 1.3 57.2 + - - +
113B LEU* 2.9 56.5 + - + +
114B PRO* 3.4 1.4 - - - +
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Residues in contact with GLU 110 (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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60B ALA 5.3 2.3 - - - +
61B TYR* 3.7 20.5 - - + -
106B GLU 3.0 18.1 + - - +
107B ALA* 3.9 6.5 - - - +
108B GLN 3.2 0.2 - - - -
109B LYS* 1.3 76.7 - - - +
111B ALA* 1.3 61.1 + - - +
114B PRO* 3.2 23.8 - - - +
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Residues in contact with ALA 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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107B ALA 3.1 17.6 + - - +
108B GLN* 3.1 6.3 + - - +
110B GLU* 1.3 79.5 - - - +
112B PHE* 1.3 72.6 + - + +
114B PRO* 4.4 0.9 - - - +
115B LYS* 5.0 6.1 - - - +
193B PHE* 3.4 23.2 - - + -
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Residues in contact with PHE 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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100B ILE* 3.7 28.0 - - + -
108B GLN* 2.9 43.2 + - + +
111B ALA* 1.3 85.8 - - + +
113B LEU* 1.3 65.1 + - - +
114B PRO* 3.4 3.5 - - - -
115B LYS* 3.4 6.5 + - - +
116B LEU* 3.2 26.2 + - + +
167B VAL* 3.9 19.1 - - + +
191B ALA* 3.5 32.5 - - + -
192B PHE* 3.9 17.0 - - - -
193B PHE* 3.3 41.1 - + - -
228B GLU 5.2 4.7 - - - -
229B ALA* 5.8 0.2 - - - -
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Residues in contact with LEU 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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57B VAL* 4.2 10.5 - - + -
61B TYR* 3.9 27.4 - - + +
97B THR* 4.0 32.3 - - + +
100B ILE* 3.9 18.6 - - + -
101B LEU* 4.1 23.6 - - + +
109B LYS* 2.9 52.9 + - + +
112B PHE* 1.3 69.3 - - - +
114B PRO* 1.3 60.0 - - + +
116B LEU* 3.8 5.3 - - + +
117B ALA* 2.7 35.0 + - - +
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Residues in contact with PRO 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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61B TYR* 3.6 21.5 - - + +
62B GLY* 5.1 5.0 - - - +
109B LYS 3.4 5.4 - - - +
110B GLU* 3.2 41.3 - - - +
111B ALA 4.4 1.3 - - - +
112B PHE 3.5 3.1 - - - -
113B LEU* 1.3 92.2 - - + +
115B LYS* 1.3 62.6 + - + +
117B ALA* 4.1 1.7 - - + +
118B SER* 3.3 23.7 + - - -
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Residues in contact with LYS 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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111B ALA 5.0 3.6 + - - +
112B PHE 3.4 7.7 + - - +
113B LEU 3.3 0.4 - - - -
114B PRO* 1.3 79.3 - - + +
116B LEU* 1.3 65.3 + - + +
118B SER* 3.3 7.0 + - - -
120B GLU* 3.2 20.9 + - + -
121B ALA* 3.1 38.6 + - + +
167B VAL* 5.5 0.7 - - + -
193B PHE* 3.7 37.0 - - + -
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Residues in contact with LEU 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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53B PHE 3.0 2.9 - - - +
92B HIS* 2.9 27.5 + - + -
96B ALA* 4.8 0.7 - - + +
97B THR* 3.7 30.1 - - + +
100B ILE* 3.7 30.3 - - + -
112B PHE* 3.2 23.6 + - + +
113B LEU* 3.8 8.7 - - + +
115B LYS* 1.3 78.7 - - - +
117B ALA* 1.3 61.8 + - - +
119B GLY 3.3 9.2 + - - -
121B ALA 3.4 16.4 - - - +
123B GLY* 3.7 27.8 - - - +
167B VAL* 3.8 20.9 - - + -
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Residues in contact with ALA 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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48B ALA 5.1 1.2 - - - +
51B GLY* 4.7 7.8 - - - +
53B PHE* 3.5 13.2 + - - +
54B GLY* 3.5 27.2 + - - -
57B VAL* 4.2 11.0 - - + -
62B GLY 3.5 31.1 - - - +
63B GLY* 3.9 4.8 - - - +
97B THR* 5.4 0.2 - - - +
113B LEU 2.7 22.6 + - - +
114B PRO 4.1 1.6 - - - +
116B LEU* 1.3 74.1 - - - +
118B SER* 1.3 58.8 + - - +
119B GLY 3.3 0.2 - - - -
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Residues in contact with SER 118 (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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48B ALA* 3.3 23.8 - - - +
53B PHE* 4.7 0.2 - - - -
62B GLY 5.3 2.7 - - - -
114B PRO 3.3 14.6 + - - -
115B LYS* 3.3 5.5 + - - -
116B LEU 3.3 0.2 - - - -
117B ALA* 1.3 77.0 - - - +
119B GLY* 1.3 58.5 + - - +
120B GLU* 2.9 38.2 + - - +
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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