Contacts of the helix formed by residues 309 - 315 (chain F) in PDB entry 3IKM
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 309 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282F GLU* 4.9 12.4 + - - -
306F LEU* 3.4 17.9 + - + +
307F GLY 3.6 5.3 + - - +
308F ASP* 1.3 76.6 + - - +
310F GLU* 1.3 80.2 + - - +
311F LEU* 3.7 1.2 - - - +
312F LEU* 3.1 28.6 - - + +
313F HIS* 3.4 13.7 + - - +
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Residues in contact with GLU 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F LEU* 6.6 0.4 - - + -
190F LEU* 5.0 10.8 - - + -
306F LEU* 2.7 53.2 - - + +
309F HIS* 1.3 85.2 - - - +
311F LEU* 1.3 61.0 + - + +
312F LEU 3.1 1.1 - - - -
313F HIS* 2.7 21.3 - - + +
314F MET* 2.3 41.7 + - + +
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Residues in contact with LEU 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F LEU* 4.1 22.2 - - + -
193F TYR* 3.3 41.1 - - + -
242F PHE* 3.9 25.1 - - + -
308F ASP* 4.5 17.3 - - - +
310F GLU* 1.3 81.7 - - + +
312F LEU* 1.3 60.9 + - + +
314F MET* 2.6 9.8 + - + -
315F TYR* 2.3 41.7 + - + +
321F LYS* 5.7 5.4 - - + -
332F VAL* 5.5 9.4 - - + -
333F PRO* 4.5 9.6 - - + +
334F CYS 5.2 1.8 - - - +
335F VAL* 6.1 2.0 - - - -
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Residues in contact with LEU 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308F ASP 3.0 29.8 - - - +
309F HIS* 3.1 31.0 - - + +
311F LEU* 1.3 81.7 - - + +
313F HIS* 1.3 69.8 + - - +
315F TYR 2.7 22.2 + - - -
316F PRO* 3.6 4.0 - - - +
321F LYS* 4.9 14.6 - - - +
332F VAL* 4.9 16.1 - - + +
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Residues in contact with HIS 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F LEU 4.2 11.0 + - - -
140F PRO* 3.3 25.9 + - + -
142F ASP* 5.1 4.7 + - - -
309F HIS 3.4 5.5 + - - +
310F GLU* 2.7 36.5 - - + +
312F LEU* 1.3 79.9 - - - +
314F MET* 1.3 64.1 + - + +
316F PRO* 4.1 9.5 - - - +
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Residues in contact with MET 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F HIS* 4.5 14.6 - - + -
190F LEU* 3.0 45.8 - - + +
191F GLU* 3.3 26.2 - - - +
310F GLU* 2.3 35.6 + - + +
311F LEU* 2.6 21.2 + - + +
313F HIS* 1.3 73.4 - - + +
315F TYR* 1.3 105.7 + - + +
316F PRO* 3.3 8.5 - - - +
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Residues in contact with TYR 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F LEU 4.7 2.5 - - - -
191F GLU* 2.6 55.7 + - + +
193F TYR* 5.3 6.5 - + - -
194F VAL* 5.4 11.9 - - + -
311F LEU* 2.3 30.5 + - + +
312F LEU* 2.7 7.4 + - - +
314F MET* 1.3 108.3 - - + -
316F PRO* 1.3 70.5 - - + +
321F LYS* 3.5 41.4 + - + +
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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