Contacts of the helix formed by residues 202 - 210 (chain J) in PDB entry 1MKD
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 HIS 202 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509F GLN 5.9 1.1 - - - -
192J GLU* 4.5 8.2 - - - +
200J GLY 3.3 4.1 + - - +
201J LEU* 1.3 75.6 - - - +
203J VAL* 1.3 59.7 + - - +
204J PHE* 3.2 37.8 + + + -
205J ARG* 3.1 55.1 + - + +
206J ILE* 3.3 24.6 + - - +
424J GLN* 3.1 28.2 + - - -
425J LEU* 4.1 12.0 - - + +
428J GLN* 3.8 4.9 + - - -
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Residues in contact with VAL 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201J LEU* 2.9 15.2 + - + +
202J HIS* 1.3 70.6 - - - +
204J PHE* 1.3 72.6 + - + +
206J ILE* 3.3 11.0 + - - +
207J ALA* 2.8 26.7 + - - +
214J PRO* 4.5 2.6 - - + +
218J ILE* 4.0 23.1 - - + -
260J ILE* 3.8 26.2 - - + +
263J ALA* 4.2 6.3 - - + -
264J ASP* 4.4 16.8 - - + +
267J GLN* 6.5 0.4 - - + -
425J LEU* 4.7 4.7 - - + +
429J TRP* 4.0 25.4 - - + +
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Residues in contact with PHE 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202J HIS* 3.2 11.7 + - + -
203J VAL* 1.3 75.0 - - + +
205J ARG* 1.3 66.7 + - - +
207J ALA* 3.2 18.7 - - - +
208J GLU* 3.3 14.7 + - - +
260J ILE* 4.0 13.5 - - + -
425J LEU* 3.8 17.9 - - + -
428J GLN* 3.4 47.6 - - + +
429J TRP* 3.5 52.9 - + - -
432J ARG* 3.1 39.9 - - - -
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Residues in contact with ARG 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509F GLN 4.8 1.2 + - - -
510F SER* 3.1 41.0 + - - +
188J VAL* 5.7 3.8 - - - -
192J GLU* 3.0 29.9 + - - +
202J HIS* 3.1 50.4 + - + +
204J PHE* 1.3 75.2 - - - +
206J ILE* 1.3 64.3 + - - +
208J GLU* 2.9 17.3 + - - +
209J LEU* 2.9 42.3 + - + +
424J GLN* 4.5 3.0 - - - +
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Residues in contact with ILE 206 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189J LEU* 3.9 10.7 - - + +
192J GLU* 3.7 24.2 - - + -
193J LEU* 3.9 30.7 - - + -
201J LEU* 3.6 39.0 - - + -
202J HIS 3.3 13.8 + - - +
203J VAL* 3.5 9.6 - - - +
205J ARG* 1.3 78.0 - - - +
207J ALA* 1.3 51.7 + - - +
209J LEU* 3.9 6.9 - - - -
210J SER* 2.7 35.0 + - - -
214J PRO* 4.5 6.1 - - + -
217J VAL* 4.5 6.1 - - + -
218J ILE* 4.3 15.9 - - + -
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Residues in contact with ALA 207 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203J VAL 2.8 13.6 + - - +
204J PHE* 3.2 15.9 - - + +
205J ARG 3.0 0.2 - - - -
206J ILE* 1.3 77.4 - - - +
208J GLU* 1.3 56.3 + - + +
210J SER* 3.1 9.0 + - - -
212J ASN* 2.7 35.7 + - - +
214J PRO* 3.9 23.1 - - + -
260J ILE* 4.2 20.0 - - + -
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Residues in contact with GLU 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204J PHE 3.3 14.1 + - - +
205J ARG* 2.9 17.5 + - - +
207J ALA* 1.3 74.3 - - + +
209J LEU* 1.3 58.1 + - + +
210J SER 2.8 14.8 + - - -
211J GLY* 2.8 16.3 + - - -
212J ASN 4.8 0.7 - - - +
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Residues in contact with LEU 209 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185J GLN* 4.2 39.5 - - + +
186J GLU* 5.7 2.4 - - - +
188J VAL* 4.0 13.7 - - + -
189J LEU* 3.5 42.9 - - + +
192J GLU* 3.8 29.2 - - + -
205J ARG* 2.9 33.5 + - + +
206J ILE* 4.6 1.6 - - - +
208J GLU* 1.3 76.9 - - + +
210J SER* 1.3 56.1 + - - +
211J GLY 3.5 0.7 - - - -
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Residues in contact with SER 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189J LEU* 3.9 8.5 - - - -
206J ILE 2.7 21.4 + - - -
207J ALA 3.1 3.6 + - - -
208J GLU 2.8 1.4 + - - -
209J LEU* 1.3 77.7 - - - +
211J GLY* 1.3 62.8 + - - +
213J ARG* 2.9 38.3 + - - +
214J PRO 3.4 0.9 - - - -
217J VAL* 3.6 28.5 - - - -
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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