Contacts of the helix formed by residues 348 - 359 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273C GLY* 4.6 0.7 - - - -
311C ARG* 4.0 0.2 - - - -
336C PHE 2.7 28.3 + - - -
337C ALA 3.4 8.5 + - - -
338C PHE* 3.6 22.7 - - - -
345C THR 2.9 18.0 + - - -
346C ARG 3.1 1.0 - - - -
347C GLU* 1.3 78.2 - - - +
349C SER* 1.3 63.6 + - - +
350C SER* 3.1 12.7 + - - -
351C ILE* 3.0 27.9 + - - +
352C TYR* 3.4 5.5 - - - -
442C ARG* 5.9 0.2 + - - -
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Residues in contact with SER 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C VAL* 3.7 28.3 - - - -
271C GLY* 2.6 32.0 + - - -
273C GLY* 5.0 1.0 - - - -
311C ARG* 2.9 31.1 + - - +
338C PHE* 5.2 1.8 + - - +
347C GLU 3.4 2.2 + - - -
348C SER* 1.3 73.6 + - - +
350C SER* 1.3 62.8 + - - +
352C TYR* 3.0 3.9 + - - +
353C ILE* 2.9 27.0 + - - +
414C CYS* 5.2 1.3 - - - -
442C ARG* 5.3 4.6 - - - +
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Residues in contact with SER 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C ILE* 4.8 1.8 - - - -
335C GLY 2.8 28.1 + - - -
336C PHE* 3.4 22.9 - - - -
348C SER* 3.1 13.7 + - - -
349C SER* 1.3 79.2 - - - +
351C ILE* 1.3 55.6 + - - +
353C ILE* 4.0 0.4 - - - +
354C SER* 2.7 37.6 + - - -
414C CYS* 3.1 28.0 + - - +
415C THR* 3.5 4.9 + - - -
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Residues in contact with ILE 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C PHE* 3.7 26.7 - - + -
345C THR 3.4 25.6 - - - +
346C ARG* 5.3 0.2 - - - -
347C GLU* 4.5 6.5 - - - +
348C SER* 3.0 18.1 + - - +
350C SER* 1.3 77.1 - - - +
352C TYR* 1.3 72.1 + - + +
354C SER* 3.3 2.6 + - - -
355C LYS* 2.8 43.2 + - + +
379C ASP* 3.9 39.5 - - + +
380C LEU* 3.9 6.9 - - + +
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Residues in contact with TYR 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C GLN* 4.6 5.8 + - - -
311C ARG* 3.4 42.6 - - + -
347C GLU* 2.5 38.4 + - - -
348C SER 3.4 17.0 - - - -
349C SER 3.0 5.4 + - - +
351C ILE* 1.3 86.1 - - + +
353C ILE* 1.3 66.9 + - - +
355C LYS* 3.1 13.7 + - + +
356C TYR* 2.9 40.3 + + + -
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Residues in contact with ILE 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C VAL* 3.8 27.8 - - + -
311C ARG* 3.4 36.1 - - + +
314C PHE* 4.1 7.6 - - + -
315C ALA* 4.3 9.6 - - + +
318C ILE* 4.3 9.0 - - + -
333C ILE* 4.9 2.0 - - + -
349C SER 2.9 19.7 + - - +
350C SER 4.2 2.5 - - - +
352C TYR* 1.3 75.8 - - - +
354C SER* 1.3 63.5 + - - +
356C TYR* 3.3 6.2 + - + +
357C LEU* 3.2 38.1 + - + +
412C VAL* 4.3 20.2 - - + -
414C CYS* 4.3 11.0 - - - -
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Residues in contact with SER 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C ILE* 4.0 16.7 - - - +
336C PHE* 4.0 9.2 - - - -
350C SER 2.7 23.2 + - - -
351C ILE 3.6 3.6 - - - -
353C ILE* 1.3 78.4 - - - +
355C LYS* 1.3 57.4 + - - +
357C LEU* 3.0 7.6 + - - +
358C MET* 2.9 31.5 + - - +
364C LEU* 3.6 23.6 - - - +
366C ILE* 4.4 1.6 - - - +
380C LEU* 3.9 19.1 - - - -
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Residues in contact with LYS 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C ILE* 2.8 29.5 + - + +
352C TYR* 3.1 14.1 + - + +
354C SER* 1.3 77.6 - - - +
356C TYR* 1.3 61.2 + - - +
358C MET* 3.3 12.7 + - + +
359C ASP* 2.9 34.0 + - - +
379C ASP 3.9 21.7 + - - -
380C LEU* 4.2 23.3 - - + +
381C SER 4.6 8.9 + - - -
382C HIS* 5.1 15.1 + - - -
383C PRO* 5.6 4.0 - - - +
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Residues in contact with TYR 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C ASP* 4.8 3.5 + - - +
311C ARG* 4.4 6.7 - - + -
312C ARG* 3.9 47.2 + - + +
315C ALA* 3.7 30.5 - - + -
319C ILE* 4.3 2.3 - - + +
352C TYR* 2.9 34.6 + + + -
353C ILE* 3.7 8.5 - - + +
354C SER 3.3 0.4 - - - -
355C LYS* 1.3 78.9 - - + +
357C LEU* 1.3 61.7 + - - +
359C ASP* 3.5 19.5 + - + +
360C GLU* 3.4 19.4 - - - +
98E MET* 4.3 15.4 - - + +
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Residues in contact with LEU 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C ALA* 4.8 2.5 - - + +
318C ILE* 4.2 25.1 - - + -
319C ILE* 3.9 28.7 - - + -
326C VAL* 5.0 4.7 - - + -
331C ILE* 4.4 17.7 - - + -
333C ILE* 4.0 26.5 - - + -
353C ILE* 3.4 24.5 - - + +
354C SER 3.0 6.3 + - - +
356C TYR* 1.3 76.4 - - + +
358C MET* 1.3 66.4 + - - +
359C ASP 3.1 1.3 - - - -
360C GLU* 2.9 16.3 + - - +
362C ALA* 3.2 22.2 + - + +
364C LEU* 4.0 19.1 - - + -
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Residues in contact with MET 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C SER 2.9 23.2 + - - +
355C LYS* 3.7 11.2 - - + +
357C LEU* 1.3 74.9 - - - +
359C ASP* 1.3 59.3 + - - +
361C GLY* 2.8 21.6 + - - +
362C ALA 4.5 2.5 - - - +
364C LEU* 3.8 15.0 - - + +
380C LEU* 4.0 38.6 - - - +
390C GLN* 3.5 44.0 + - + +
391C VAL* 4.3 5.2 - - + +
394C LEU* 3.6 23.8 - - + +
395C VAL* 3.9 26.9 - - + -
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Residues in contact with ASP 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C LYS* 2.9 26.3 + - - +
356C TYR* 3.5 20.9 - - + +
357C LEU 3.1 0.4 - - - -
358C MET* 1.3 77.4 - - - +
360C GLU* 1.3 56.6 + - - +
390C GLN* 4.2 15.1 + - - +
96E TYR* 3.2 30.0 - - - +
97E GLY* 3.8 14.4 + - - +
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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