Contacts of the helix formed by residues 110 - 115 (chain D) in PDB entry 3KDO
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 GLY 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D LEU 3.6 1.7 + - - -
106D ALA* 3.5 17.7 + - - -
107D SER 4.2 1.4 + - - -
108D ILE 3.9 0.2 - - - -
109D ALA* 1.3 78.5 - - - +
111D ASN* 1.3 64.5 + - - -
112D ILE* 3.1 7.7 + - - +
113D PHE* 3.4 17.8 + - - +
114D GLY 4.8 0.2 + - - -
283J ALA* 3.9 7.4 - - - -
284J MET* 3.5 24.6 + - - -
286J ALA* 5.4 1.2 - - - +
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Residues in contact with ASN 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D GLU* 3.2 25.6 + - + +
106D ALA 4.6 1.8 + - - -
107D SER 5.7 0.2 + - - -
110D GLY* 1.3 72.0 - - - +
112D ILE* 1.3 62.3 + - - +
113D PHE 3.1 0.4 - - - -
114D GLY* 2.9 15.1 + - - -
115D MET* 3.7 6.4 + - - +
192J GLU* 2.5 42.1 + - - +
281J HIS* 3.2 21.0 - - - -
283J ALA* 3.7 8.1 - - - +
284J MET 5.1 0.4 - - - +
285J HIS* 6.0 1.8 - - - -
286J ALA* 6.4 0.2 - - - -
323J LEU* 4.0 16.5 - - + +
600J CAP 3.3 26.0 + - - +
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Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D PHE* 3.5 37.9 - - + -
46D VAL* 3.5 26.5 - - + +
49D GLU* 3.7 20.6 - - + +
50D SER* 4.0 9.4 - - - -
107D SER 4.3 4.0 - - - +
108D ILE* 3.5 20.9 - - - +
109D ALA* 4.0 2.7 - - - +
110D GLY 4.0 12.8 - - - +
111D ASN* 1.3 78.3 - - - +
113D PHE* 1.3 66.0 + - + +
114D GLY 3.3 0.7 + - - -
115D MET* 3.2 33.7 + - + +
118D VAL* 4.2 3.6 - - - +
121D LEU* 3.2 18.3 - - + +
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Residues in contact with PHE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D PHE* 5.1 3.1 - + - -
109D ALA* 3.5 35.0 - - + -
110D GLY 3.4 17.7 + - - +
111D ASN 3.0 1.2 + - - -
112D ILE* 1.3 78.9 - - + +
114D GLY* 1.3 57.7 + - - +
115D MET 3.5 0.4 - - - -
118D VAL* 4.7 1.0 - - - +
121D LEU* 3.3 38.6 - - + -
123D LEU* 4.3 12.8 - - + -
294D HIS* 3.3 19.2 - + + -
295D GLY* 3.2 28.9 - - - -
296D ILE* 3.6 19.7 - - + -
284J MET 4.6 1.8 - - - -
286J ALA* 3.5 17.9 - - + +
287J ALA* 3.7 21.8 - - + +
290J ARG* 2.9 21.2 + - - -
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Residues in contact with GLY 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ASN 2.9 8.2 + - - -
113D PHE* 1.3 79.7 - - - +
115D MET* 1.3 62.5 + - - +
285J HIS* 5.8 1.6 - - - -
286J ALA* 3.5 17.0 - - - +
290J ARG* 3.7 6.1 - - - -
323J LEU* 3.5 11.8 - - - -
324J GLU* 2.9 34.7 + - - +
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Residues in contact with MET 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ALA* 4.0 18.6 - - + +
46D VAL* 3.4 37.0 - - + +
49D GLU* 3.9 28.7 - - + -
111D ASN 3.7 9.3 + - - +
112D ILE* 3.2 26.2 + - - +
113D PHE 3.5 2.2 - - - -
114D GLY* 1.3 75.0 - - - +
116D LYS* 1.3 63.6 + - - +
117D ARG* 3.0 10.3 + - + +
118D VAL* 3.2 29.9 + - + +
290J ARG* 3.2 7.2 + - - -
322J LYS* 4.0 5.8 - - + +
323J LEU* 3.8 13.7 - - + -
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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