Contacts of the helix formed by residues 104 - 114 (chain B) in PDB entry 3OPY
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 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B SER 4.0 0.4 + - - -
103B SER* 1.4 83.8 + - - +
105B LEU* 1.4 66.0 + - - +
106B SER* 3.3 13.7 + - - +
107B LYS* 3.5 20.9 + - - +
108B LEU* 4.1 3.8 + - - +
151B ALA 4.7 4.2 + - - -
153B ASN* 3.8 27.2 - - - +
154B GLU 4.8 2.4 + - - -
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Residues in contact with LEU 105 (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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102B SER* 3.7 15.0 - - - +
103B SER 3.7 0.9 - - - -
104B SER* 1.4 71.2 - - - +
106B SER* 1.4 64.3 + - - +
108B LEU* 3.1 11.3 + - - +
109B VAL* 3.0 28.3 + - + +
126B ILE* 3.8 21.1 - - + +
127B SER* 3.2 24.9 - - - +
129B PHE* 3.9 17.9 - - + +
140B LEU* 3.3 38.4 - - + +
141B ILE 4.1 1.1 - - - -
142B GLY* 3.7 23.3 - - - +
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B SER* 4.1 13.0 - - - -
105B LEU* 1.4 73.1 + - - +
107B LYS* 1.4 59.5 + - - +
109B VAL* 3.5 8.7 + - - +
110B LYS* 3.3 23.0 + - - +
121B GLN* 6.0 0.9 - - - +
125B GLU 5.0 14.1 + - - -
126B ILE* 5.5 6.2 - - - +
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B SER* 3.5 16.3 + - - +
105B LEU 3.2 0.8 - - - -
106B SER* 1.4 77.2 + - - +
108B LEU* 1.3 63.3 + - - +
110B LYS* 3.7 5.8 + - - +
111B LEU* 3.3 22.5 + - - +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE 5.8 4.3 - - - +
34B LEU* 6.4 2.2 - - + -
102B SER* 5.9 3.1 - - - +
104B SER 4.1 2.1 + - - +
105B LEU* 3.1 15.3 + - - +
107B LYS* 1.3 76.1 - - - +
109B VAL* 1.4 59.8 + - + +
111B LEU* 3.3 8.3 + - - +
112B LEU* 2.9 42.4 + - + +
140B LEU* 5.6 11.9 - - + -
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 3.0 21.3 + - + +
106B SER* 3.8 7.4 - - - +
107B LYS 3.4 0.2 - - - -
108B LEU* 1.4 74.3 - - - +
110B LYS* 1.4 55.5 + - - +
112B LEU* 3.4 4.3 + - + +
113B LYS* 3.0 32.6 + - + +
119B VAL* 4.0 22.1 - - + +
121B GLN* 3.5 39.7 - - - +
126B ILE* 5.8 0.7 - - + -
129B PHE* 3.7 27.6 - - + -
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Residues in contact with LYS 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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106B SER 3.3 14.1 + - - +
107B LYS* 3.9 7.0 - - - +
108B LEU 3.3 0.2 - - - -
109B VAL* 1.4 78.9 - - - +
111B LEU* 1.4 55.1 + - - +
113B LYS* 4.6 3.4 - - - -
114B ASP* 3.0 44.4 + - - +
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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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33B PHE* 3.6 20.6 - - + +
107B LYS 3.3 16.5 + - - +
108B LEU* 3.3 9.2 + - - +
110B LYS* 1.4 77.9 - - - +
112B LEU* 1.4 57.8 + - - +
114B ASP* 4.3 2.7 - - - +
115B GLY* 3.3 14.6 + - - -
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Residues in contact with LEU 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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29B PHE* 3.9 19.5 - - + -
33B PHE* 3.8 26.2 - - + -
34B LEU* 5.9 7.2 - - + -
108B LEU* 2.9 26.9 + - + +
109B VAL* 3.7 4.5 - - + +
111B LEU* 1.4 74.1 - - - +
113B LYS* 1.4 56.3 + - - +
115B GLY* 3.0 13.9 + - - -
116B GLY 3.1 0.5 + - - -
117B HIS* 2.8 47.5 + - + +
119B VAL* 3.9 22.4 - - + -
129B PHE* 5.9 1.3 - - + -
131B VAL* 3.8 22.9 - - + -
140B LEU* 5.3 11.0 - - + -
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Residues in contact with LYS 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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109B VAL* 3.0 21.1 + - + +
110B LYS* 4.0 4.5 - - - +
112B LEU* 1.4 73.2 - - - +
114B ASP* 1.4 61.3 + - - +
116B GLY* 3.3 18.0 + - - -
117B HIS 3.5 12.8 + - - +
119B VAL* 4.4 5.8 - - + +
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Residues in contact with ASP 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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110B LYS* 3.0 33.3 + - - +
111B LEU* 4.7 3.1 - - - +
113B LYS* 1.4 76.1 - - - +
115B GLY* 1.3 56.5 + - - +
116B GLY 3.2 3.4 + - - -
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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