Contacts of the helix formed by residues 204 - 209 (chain M) in PDB entry 1KYO
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 204 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M VAL* 4.2 11.2 - - - -
103M ASN* 3.9 20.2 - - - +
106M ALA* 4.5 1.6 - - - -
200M PHE 3.4 12.1 - - - -
201M VAL* 2.5 24.7 + - - -
203M GLU* 1.3 81.5 - - - +
205M LEU* 1.3 63.2 + - - +
206M LEU* 2.9 28.0 + - - +
207M SER* 3.0 19.1 + - - -
208M THR* 4.2 3.4 + - - -
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Residues in contact with LEU 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M ASN* 4.4 10.3 - - - +
106M ALA* 4.0 19.0 - - + +
107M ASP* 4.7 12.3 - - - +
110M TYR* 3.3 39.4 - - + +
111M LYS* 3.6 29.6 - - + -
204M SER* 1.3 77.8 - - - +
206M LEU* 1.3 59.7 + - - +
207M SER 3.2 0.9 - - - -
208M THR* 3.9 13.5 - - - +
209M LEU* 3.1 28.0 + - - +
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Residues in contact with LEU 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M LEU* 4.9 9.0 - - + +
33M VAL* 5.1 5.2 - - + -
102M VAL* 4.2 15.3 - - + +
105M LEU* 5.0 2.2 - - + -
106M ALA* 3.6 25.6 - - + +
109M LEU* 3.7 29.2 - - + -
182M LYS* 3.3 24.6 - - - +
185M LEU* 4.4 16.6 - - + -
187M VAL* 4.8 11.0 - - + -
201M VAL* 3.8 21.5 - - + -
204M SER* 2.9 22.6 + - - +
205M LEU* 1.3 78.6 - - - +
207M SER* 1.3 57.6 + - - +
208M THR 3.5 0.2 - - - -
209M LEU* 3.7 17.4 - - + +
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Residues in contact with SER 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M LEU* 6.3 0.7 - - - -
182M LYS* 3.5 27.4 + - - +
201M VAL* 4.3 4.9 + - - +
202M ASP* 4.0 21.8 - - - -
203M GLU* 4.2 8.5 + - - -
204M SER 3.0 15.0 + - - -
206M LEU* 1.3 78.1 - - - +
208M THR* 1.3 62.9 + - - +
209M LEU 3.2 2.9 + - - +
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Residues in contact with THR 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M TYR* 3.9 32.0 + - + +
204M SER 4.3 1.6 + - - -
205M LEU* 3.7 19.9 + - + +
206M LEU 3.5 0.2 - - - -
207M SER* 1.3 81.3 + - - +
209M LEU* 1.3 63.1 + - - +
210M PRO* 3.7 4.2 - - - +
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Residues in contact with LEU 209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M ALA* 5.8 0.4 - - - +
109M LEU* 4.2 13.9 - - + +
110M TYR* 3.8 39.0 - - + +
180M TYR 4.0 14.6 - - - +
182M LYS* 3.2 26.1 - - + +
185M LEU* 4.4 15.9 - - + -
205M LEU 3.1 20.3 + - - +
206M LEU* 3.7 38.4 - - + +
207M SER 3.2 0.9 - - - +
208M THR* 1.3 80.0 - - - +
210M PRO* 1.3 78.9 - - + +
211M ALA 3.5 1.4 + - - -
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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