Contacts of the helix formed by residues 344 - 353 (chain B) 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 ARG 344 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B LEU 4.2 9.8 + - - +
92B LEU* 3.8 37.4 + - + +
94B GLY* 3.6 8.7 - - - +
234B LYS* 3.0 34.8 - - - +
299B LEU 6.0 1.6 - - - +
341B ASP* 2.7 37.5 + - - +
342B LEU 2.4 7.7 + - - -
343B ASP* 1.3 106.7 + - - +
345B GLY* 1.3 53.5 + - - +
346B MET 2.8 6.3 - - - +
347B LEU* 2.6 49.0 + - + +
348B ALA* 3.1 6.4 + - - +
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Residues in contact with GLY 345 (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 LEU* 4.1 9.8 - - - +
263B TRP* 4.4 13.3 + - - -
300B ILE* 6.3 4.7 - - - -
341B ASP 3.7 4.8 + - - -
342B LEU* 2.2 37.5 + - - -
344B ARG* 1.3 67.8 - - - +
346B MET* 1.3 55.7 + - - -
348B ALA* 4.1 7.2 + - - +
349B TYR* 3.9 21.3 + - - +
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Residues in contact with MET 346 (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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99B PHE* 6.2 5.6 - - + -
103B GLY* 3.2 40.4 - - - +
106B LEU* 3.6 22.7 - - + +
107B ARG* 3.4 42.6 - - + +
110B LEU* 3.9 9.6 - - + -
342B LEU* 3.9 11.2 - - - +
343B ASP 3.5 19.1 - - - +
345B GLY* 1.3 76.0 - - - +
347B LEU* 1.3 58.6 + - + +
348B ALA 3.1 1.8 - - - -
349B TYR* 3.3 7.1 + - - +
350B LEU* 2.7 36.4 + - - +
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Residues in contact with LEU 347 (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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79B LEU* 5.1 10.5 - - + -
91B LEU* 4.7 36.3 - - + +
96B HIS* 6.2 2.9 - - + -
293B PHE* 4.6 10.5 - - + -
343B ASP 5.5 1.8 - - - +
344B ARG* 2.6 38.6 + - + +
346B MET* 1.3 75.6 - - + +
348B ALA* 1.3 56.4 + - - +
350B LEU* 2.7 39.1 - - + +
351B TYR* 3.8 6.6 + - + -
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Residues in contact with ALA 348 (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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273B PHE* 5.4 4.9 - - + -
291B TYR* 4.0 31.1 + - + -
293B PHE* 3.8 19.4 - - + -
300B ILE* 5.1 9.9 - - + -
344B ARG 3.1 5.6 + - - +
345B GLY* 4.2 9.2 - - - +
346B MET 3.1 0.2 - - - -
347B LEU* 1.3 75.3 - - - +
349B TYR* 1.3 53.5 + - - +
350B LEU 2.6 3.8 - - - -
351B TYR* 2.4 37.9 + - - +
352B ASP 3.9 2.1 + - - -
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Residues in contact with TYR 349 (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 LEU* 5.8 4.9 - - + -
110B LEU* 5.3 10.1 - - + -
263B TRP* 2.7 39.7 + + - -
264B ARG 4.5 0.7 + - - -
265B LYS* 2.5 47.4 - - + +
267B ALA* 5.8 0.2 - - - -
270B PRO* 4.8 15.1 - - + +
273B PHE* 5.1 8.7 - + - -
291B TYR* 6.0 0.7 - - - -
345B GLY 3.9 11.2 + - - +
346B MET* 3.3 10.9 + - - +
348B ALA* 1.3 77.4 - - - +
350B LEU* 1.3 55.2 + - - +
351B TYR 3.0 5.6 + - - -
352B ASP* 3.7 25.6 + - + +
353B SER* 4.1 8.3 + - - -
374B LEU* 5.0 11.2 - - + +
375B HIS* 4.1 15.8 - + + -
378B LEU* 3.7 27.8 - - + -
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Residues in contact with LEU 350 (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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69B LEU* 4.8 11.0 - - + +
73B CYS* 4.8 14.8 - - + -
78B PHE* 6.0 10.5 - - + -
106B LEU* 6.0 4.7 - - + -
346B MET 2.7 13.7 + - - +
347B LEU* 2.7 28.0 - - + +
348B ALA 2.4 6.3 + - - -
349B TYR* 1.3 73.2 - - - +
351B TYR* 1.3 83.1 + - + -
353B SER* 2.9 18.5 + - - +
372B LEU* 6.2 3.8 - - + -
374B LEU* 6.2 1.1 - - - -
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Residues in contact with TYR 351 (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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67B GLU* 3.8 16.0 - - - +
69B LEU* 3.2 42.1 - - + +
70B LEU* 4.6 4.0 - - + +
88B ARG* 5.3 4.9 + - - -
291B TYR* 3.9 10.8 - + + +
293B PHE* 3.7 33.2 - + + -
294B PRO* 4.7 18.8 - - + -
295B TRP* 6.3 1.8 - - + -
347B LEU* 4.3 8.5 - - + -
348B ALA 2.4 27.7 + - - +
350B LEU* 1.3 95.0 - - + +
352B ASP* 1.3 65.8 + - - +
353B SER* 2.9 3.6 + - - -
354B PHE* 3.6 15.0 + - - +
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Residues in contact with ASP 352 (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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268B MET* 3.2 25.9 - - - +
269B SER* 2.5 60.9 + - - -
270B PRO* 4.0 13.5 - - + +
291B TYR* 3.4 17.9 + - + +
348B ALA 3.9 0.8 + - - -
349B TYR* 3.7 24.1 + - + +
351B TYR* 1.3 76.5 - - - +
353B SER* 1.3 68.7 + - - +
354B PHE 3.3 5.7 - - - +
374B LEU* 5.8 2.8 - - - +
375B HIS* 5.7 3.5 + - - +
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Residues in contact with SER 353 (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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268B MET* 4.9 7.5 - - - +
349B TYR 4.1 6.8 + - - -
350B LEU* 2.9 26.8 + - - +
351B TYR 3.8 0.5 - - - -
352B ASP* 1.3 88.0 + - - +
354B PHE* 1.3 75.6 + - - +
372B LEU* 5.6 7.6 - - - +
373B LYS* 3.4 33.1 + - - +
374B LEU* 4.8 11.0 - - - +
436B SER* 5.5 0.4 - - - -
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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