Contacts of the helix formed by residues 348 - 360 (chain F) in PDB entry 3KHU
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 348 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273F GLY* 4.6 0.2 - - - -
311F ARG* 4.0 0.2 - - - -
336F PHE 2.8 27.1 + - - -
337F ALA 3.2 10.2 + - - -
338F PHE* 3.5 21.7 - - - -
345F THR* 3.0 17.6 + - - -
346F ARG 3.0 1.4 + - - -
347F GLU* 1.3 78.3 - - - +
349F SER* 1.3 66.4 + - - +
350F SER* 3.2 9.8 + - - -
351F ILE* 2.9 27.7 + - - +
352F TYR* 3.4 5.0 - - - -
442F ARG* 5.8 0.3 + - - -
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Residues in contact with SER 349 (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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270F VAL* 3.7 27.4 - - - -
271F GLY* 2.6 32.9 + - - -
273F GLY* 5.0 1.2 - - - +
311F ARG* 3.0 30.0 + - - +
338F PHE* 5.1 2.0 + - - +
347F GLU 3.5 2.2 + - - -
348F SER* 1.3 73.0 + - - +
350F SER* 1.3 57.4 + - - +
352F TYR* 3.2 3.6 + - - +
353F ILE* 2.9 32.8 + - - +
414F CYS* 5.2 1.6 - - - -
442F ARG* 5.3 4.4 - - - +
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Residues in contact with SER 350 (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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333F ILE* 4.9 1.9 - - - +
335F GLY 2.9 26.8 + - - -
336F PHE* 3.5 27.6 - - - -
337F ALA 4.2 0.2 + - - -
348F SER* 3.0 8.9 + - - -
349F SER* 1.3 76.9 - - - +
351F ILE* 1.3 61.8 + - - +
353F ILE* 4.2 0.4 - - - +
354F SER* 2.7 34.5 + - - -
414F CYS* 3.1 26.8 + - - +
415F THR* 3.5 5.0 + - - -
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Residues in contact with ILE 351 (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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336F PHE* 3.8 27.8 - - + -
345F THR 3.4 25.6 - - - +
346F ARG* 5.2 0.4 - - - -
347F GLU* 4.4 6.3 - - - +
348F SER* 2.9 18.1 + - - +
350F SER* 1.3 78.7 - - - +
352F TYR* 1.3 72.1 + - + +
354F SER* 3.5 2.4 - - - -
355F LYS* 2.8 42.3 + - + +
379F ASP* 3.9 38.8 - - + +
380F LEU* 3.8 5.7 - - + +
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Residues in contact with TYR 352 (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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278F GLN* 4.7 5.0 + - - -
311F ARG* 3.4 44.9 - - + -
347F GLU* 2.5 38.2 + - - -
348F SER 3.4 17.5 - - - -
349F SER 3.2 5.2 + - - +
351F ILE* 1.3 87.2 - - + +
353F ILE* 1.3 66.5 + - - +
355F LYS* 3.1 12.2 + - + +
356F TYR* 2.9 39.6 + + + -
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Residues in contact with ILE 353 (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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270F VAL* 3.8 27.6 - - + -
311F ARG* 3.2 36.6 - - + +
314F PHE* 4.0 8.5 - - + -
315F ALA* 4.3 8.7 - - + +
318F ILE* 4.4 16.2 - - + -
333F ILE* 4.9 2.5 - - + -
349F SER 2.9 19.8 + - - +
350F SER 4.2 2.2 - - - +
352F TYR* 1.3 75.4 - - - +
354F SER* 1.3 64.3 + - - +
356F TYR* 3.3 7.3 + - + +
357F LEU* 3.2 39.1 + - + +
412F VAL* 4.4 3.1 - - + -
414F CYS* 4.4 20.2 - - - -
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Residues in contact with SER 354 (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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333F ILE* 4.1 16.7 - - - +
336F PHE* 3.9 9.9 - - - -
350F SER 2.7 23.2 + - - -
351F ILE 3.5 3.8 - - - -
353F ILE* 1.3 79.0 - - - +
355F LYS* 1.3 57.3 + - - +
357F LEU* 3.2 4.5 + - - -
358F MET* 2.9 31.8 + - - +
364F LEU* 3.6 25.8 - - - +
366F ILE* 4.4 1.2 - - - +
380F LEU* 3.8 18.6 - - - -
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Residues in contact with LYS 355 (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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351F ILE* 2.8 30.9 + - + +
352F TYR* 3.1 13.0 + - + +
354F SER* 1.3 75.4 - - - +
356F TYR* 1.3 61.9 + - + +
358F MET* 3.3 13.6 + - + +
359F ASP* 2.9 31.9 + - - +
379F ASP 3.9 21.8 + - - -
380F LEU* 4.3 21.8 - - + +
381F SER 4.5 8.8 + - - -
382F HIS* 5.2 14.9 + - - -
383F PRO* 5.6 4.2 - - - +
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Residues in contact with TYR 356 (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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98D MET* 4.2 15.6 - - + +
308F ASP* 4.7 4.0 + - - +
311F ARG* 4.4 8.5 - - + -
312F ARG* 3.9 43.3 - - + +
315F ALA* 3.7 29.2 - - + -
319F ILE* 4.5 2.2 - - + +
352F TYR* 2.9 36.2 + + + -
353F ILE* 3.7 7.4 - - + +
354F SER 3.3 0.2 - - - -
355F LYS* 1.3 76.1 - - - +
357F LEU* 1.3 63.0 + - - +
359F ASP* 3.4 22.8 + - + +
360F GLU* 3.4 19.0 + - - +
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Residues in contact with LEU 357 (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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315F ALA* 4.9 2.5 - - + +
318F ILE* 4.2 25.6 - - + -
319F ILE* 3.9 27.1 - - + -
326F VAL* 4.9 5.4 - - + -
331F ILE* 4.3 18.4 - - + -
333F ILE* 4.0 17.7 - - + -
353F ILE* 3.2 25.6 + - + +
354F SER* 3.7 5.6 - - - +
356F TYR* 1.3 75.4 - - + +
358F MET* 1.3 67.5 + - - +
360F GLU* 3.0 15.5 + - - +
361F GLY 3.2 0.2 + - - -
362F ALA* 3.1 22.4 + - + +
364F LEU* 3.9 26.5 - - + -
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Residues in contact with MET 358 (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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354F SER 2.9 24.3 + - - +
355F LYS* 3.7 11.2 - - + +
357F LEU* 1.3 76.1 - - - +
359F ASP* 1.3 54.5 + - - +
361F GLY* 2.7 24.1 + - - -
362F ALA 4.5 3.1 - - - +
364F LEU* 3.8 15.5 - - + -
380F LEU* 3.9 37.9 - - - +
390F GLN* 3.5 45.2 + - + +
391F VAL* 4.2 5.4 - - + +
394F LEU* 3.5 23.1 - - + +
395F VAL* 3.8 28.0 - - + -
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Residues in contact with ASP 359 (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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96D TYR* 3.1 30.8 - - + +
97D GLY* 3.7 14.0 + - - +
355F LYS* 2.9 24.6 + - - +
356F TYR* 3.5 19.3 - - + +
357F LEU 3.2 0.4 - - - -
358F MET* 1.3 76.2 - - - +
360F GLU* 1.3 56.7 + - - +
361F GLY 3.4 0.8 + - - -
390F GLN* 4.0 16.2 + - - +
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Residues in contact with GLU 360 (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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94D LYS* 2.6 32.7 + - - -
96D TYR* 3.5 14.6 - - - +
97D GLY* 3.4 5.8 - - - -
98D MET* 2.7 42.3 + - - +
319F ILE* 3.6 25.4 - - + +
324F ASN 4.4 0.9 - - - +
326F VAL* 3.8 19.7 + - + +
327F THR* 3.2 21.0 + - - -
356F TYR 3.4 15.4 - - - +
357F LEU* 3.0 9.7 + - - +
359F ASP* 1.3 75.2 - - - +
361F GLY* 1.3 61.8 + - - +
362F ALA 3.3 0.2 - - - -
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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