Contacts of the helix formed by residues 339 - 354 (chain C) in PDB entry 1U2Z
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 339 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C PRO* 2.7 45.6 + - + +
186C CYS 4.4 2.3 + - - -
187C LEU* 3.7 22.5 - - + +
337C ILE 3.3 2.8 + - - -
338C PRO* 1.3 72.2 - - - +
340C SER* 1.3 61.8 + - - +
341C PHE 3.3 0.9 + - - -
342C ILE* 3.9 6.6 + - - +
343C HIS* 3.6 29.6 - - + +
378C ASN* 3.1 38.9 + - - +
381C SER* 3.6 19.8 + - - +
382C ASP* 3.0 31.3 + - - +
385C GLN* 3.9 24.5 + - - +
412C GLU* 5.2 1.5 - - - +
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Residues in contact with SER 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C VAL* 4.1 10.4 - - - +
181C ASP* 5.1 4.5 + - - +
185C PRO* 4.4 3.2 + - - +
274C TYR* 3.0 15.1 + - - -
338C PRO* 3.9 11.3 - - - +
339C ARG* 1.3 78.4 - - - +
341C PHE* 1.3 60.4 + - - +
342C ILE 3.5 0.2 - - - -
343C HIS* 3.5 12.3 - - - +
344C ASP* 2.8 38.1 + - - +
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Residues in contact with PHE 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C LEU* 5.0 1.8 - - + -
194C PHE* 5.0 7.9 - + - -
271C LEU* 6.0 4.0 - - + -
274C TYR* 3.6 48.7 - + + -
278C VAL* 4.9 6.3 - - + -
279C PHE* 3.9 27.6 - + - -
337C ILE* 4.1 22.2 - - + -
338C PRO* 2.9 22.5 + - + +
340C SER* 1.3 80.6 + - - +
342C ILE* 1.3 59.7 + - + +
344C ASP* 3.6 0.7 - - - +
345C PHE* 2.7 50.1 + + + +
445C TYR* 5.3 3.8 - + - -
447C MET* 3.9 38.4 - - + -
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Residues in contact with ILE 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C LEU* 3.6 17.5 - - + -
189C LEU* 5.7 0.9 - - + -
193C LEU* 5.3 6.3 - - + -
337C ILE* 4.3 17.3 - - + -
338C PRO 4.4 0.6 + - - +
339C ARG 3.9 6.0 + - - +
340C SER 3.5 0.2 - - - -
341C PHE* 1.3 83.0 - - + +
343C HIS* 1.3 65.1 + - + +
345C PHE* 3.2 7.6 + - + +
346C LEU* 2.9 43.9 + - + +
408C GLN* 4.5 5.6 - - + -
411C LEU* 3.6 29.2 - - + +
412C GLU* 3.2 47.8 - - + +
447C MET* 6.4 0.9 - - - -
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Residues in contact with HIS 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ARG* 3.6 27.1 + - + +
340C SER* 3.5 12.5 - - - +
341C PHE 3.1 0.2 - - - -
342C ILE* 1.3 78.5 - - + +
344C ASP* 1.3 65.7 + - - +
346C LEU* 3.4 6.7 + - - +
347C HIS* 3.1 22.6 + - - +
377C PRO* 3.5 36.3 + - + +
378C ASN* 3.4 33.2 + - - -
381C SER* 2.7 28.1 + - - -
408C GLN* 3.9 14.6 - - - -
412C GLU* 3.9 5.6 + - - -
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Residues in contact with ASP 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C VAL* 4.6 1.7 - - - +
270C LYS* 3.5 34.0 - - + -
274C TYR* 2.3 41.8 + - + +
340C SER* 2.8 24.0 + - - +
341C PHE 3.8 1.8 - - - +
343C HIS* 1.3 71.9 - - - +
345C PHE* 1.3 66.5 + - - +
347C HIS* 3.3 8.3 + - - +
348C ILE* 3.1 30.3 + - + +
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Residues in contact with PHE 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C LEU* 6.1 1.1 - - + -
341C PHE* 2.7 34.8 + + + +
342C ILE* 3.5 7.4 - - - +
344C ASP* 1.3 73.6 - - - +
346C LEU* 1.3 63.5 + - - +
348C ILE* 3.3 24.4 + - + +
349C VAL* 3.3 12.5 + - + +
411C LEU* 4.0 18.2 - - + -
438C LEU* 3.7 25.1 - - + -
441C ARG* 3.7 34.3 - - + -
442C CYS* 3.9 11.7 - - - -
445C TYR* 3.5 25.4 - + - -
447C MET* 3.2 35.9 - - + -
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Residues in contact with LEU 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C ILE* 2.9 29.5 + - + +
343C HIS* 3.9 6.3 - - - +
345C PHE* 1.3 76.7 - - - +
347C HIS* 1.3 51.8 + - - +
349C VAL* 3.1 10.5 + - + +
350C TYR* 2.8 33.4 + - - +
377C PRO* 6.4 3.1 - - + -
404C ASN 4.9 1.1 - - - +
407C VAL* 3.7 24.5 - - + -
408C GLN* 3.9 39.3 - - + +
411C LEU* 4.0 13.2 - - + -
434C GLN* 4.4 4.8 - - + +
438C LEU* 3.8 26.5 - - + -
574C ARG* 6.0 2.0 - - - +
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Residues in contact with HIS 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C HIS 3.1 15.0 + - - +
344C ASP* 3.7 12.8 - - - +
345C PHE 3.2 0.4 - - - -
346C LEU* 1.3 73.0 - - - +
348C ILE* 1.3 70.7 + - + +
350C TYR* 3.2 11.9 + - - +
351C THR* 2.8 53.0 + - + +
355C HIS* 3.7 22.2 + + - -
574C ARG* 4.1 35.1 + - + +
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Residues in contact with ILE 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C GLU* 3.9 29.4 - - + +
270C LYS* 6.2 3.8 - - + -
271C LEU* 3.7 30.7 - - + -
344C ASP* 3.1 15.8 + - + +
345C PHE* 3.4 19.3 - - + +
347C HIS* 1.3 83.9 - - + +
349C VAL* 1.3 64.5 + - + +
351C THR* 2.7 26.6 + - - -
352C ARG* 3.1 30.6 + - - +
441C ARG* 4.7 17.3 - - - +
445C TYR* 5.6 1.8 - - + +
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Residues in contact with VAL 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C PHE* 3.3 13.2 + - + +
346C LEU* 3.1 11.6 + - + +
348C ILE* 1.3 78.6 - - + +
350C TYR* 1.3 57.1 + - - +
352C ARG* 3.0 23.1 + - - +
353C SER* 3.0 18.7 + - - +
434C GLN* 3.6 39.3 - - + +
437C GLU* 4.1 6.3 - - + -
438C LEU* 3.9 37.9 - - + +
441C ARG* 4.1 22.4 - - + +
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Residues in contact with TYR 350 (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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346C LEU 2.8 16.1 + - - +
347C HIS* 3.2 15.7 + - - +
349C VAL* 1.3 75.6 - - - +
351C THR* 1.3 57.5 + - - +
353C SER* 4.3 1.8 - - - -
354C ILE* 3.0 57.3 + - + +
355C HIS* 3.0 45.0 + + - -
358C ALA* 5.7 2.8 - - + +
361C LEU* 5.5 0.9 - - - +
372C TYR* 5.2 0.3 - - - -
374C GLU* 2.7 31.1 + - - -
402C VAL* 4.5 0.9 - - + -
404C ASN* 3.7 24.9 - - - -
434C GLN* 3.7 9.4 - - - +
574C ARG* 3.4 36.1 - - + +
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Residues in contact with THR 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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215C LEU* 3.8 10.6 - - - +
262C TYR* 4.1 26.0 - - + -
267C GLU* 4.4 0.6 + - - +
347C HIS* 2.8 57.8 + - + +
348C ILE* 2.7 18.9 + - - -
350C TYR* 1.3 77.3 - - - +
352C ARG* 1.3 77.4 + - - +
355C HIS* 3.9 16.6 - - + +
356C PRO* 3.4 19.8 - - - +
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Residues in contact with ARG 352 (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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210C ILE* 3.1 56.4 + - + +
212C SER* 3.4 13.2 - - - +
215C LEU* 3.8 17.3 - - - +
249C GLU* 2.6 28.4 + - - -
262C TYR* 3.3 10.1 + - - -
267C GLU* 2.9 41.9 + - - -
348C ILE* 3.1 12.3 + - - +
349C VAL* 3.0 9.8 + - - +
351C THR* 1.3 93.0 + - - +
353C SER* 1.3 57.5 + - - +
356C PRO* 4.6 7.0 - - - +
437C GLU* 3.6 21.1 - - + +
441C ARG* 3.0 19.8 - - - +
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Residues in contact with SER 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ILE* 5.0 3.1 - - - -
349C VAL* 3.0 15.0 + - - +
351C THR 3.3 0.8 - - - -
352C ARG* 1.3 82.3 - - - +
354C ILE* 1.3 66.8 + - - +
355C HIS 3.9 0.2 - - - -
356C PRO* 4.1 6.9 - - - +
357C GLN* 4.8 4.3 + - - -
430C LEU* 3.6 18.2 - - - +
433C LEU* 3.9 18.7 - - - +
434C GLN* 3.2 42.1 - - - +
437C GLU* 4.8 4.7 - - - -
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Residues in contact with ILE 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C TYR* 3.0 52.9 + - + +
353C SER* 1.3 79.7 + - - +
355C HIS* 1.3 67.2 + - - +
356C PRO 3.3 2.0 - - - -
357C GLN* 3.0 7.4 + - - +
358C ALA* 3.0 22.5 + - + -
361C LEU* 4.3 21.3 - - + -
402C VAL* 3.9 14.1 - - + -
430C LEU* 3.6 42.3 - - + +
434C GLN* 3.8 23.1 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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