Contacts of the helix formed by residues 317 - 334 (chain C) in PDB entry 4U1D
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 THR 317 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315C ARG 4.1 2.9 - - - +
316C ALA* 1.3 73.5 - - - +
318C GLU* 1.3 61.4 + - - +
319C GLU* 3.7 10.2 + - - +
320C GLU* 3.1 44.5 + - - +
321C PHE* 3.0 18.4 + - - -
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Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C ALA 3.8 1.2 + - - -
317C THR* 1.3 69.6 - - - +
319C GLU* 1.3 60.3 + - - +
320C GLU 3.1 0.4 - - - -
321C PHE* 3.4 9.2 + - - +
322C LYS* 2.9 28.3 + - + +
379C LYS* 3.7 34.2 - - - +
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Residues in contact with GLU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C THR* 3.2 10.8 - - - +
318C GLU* 1.3 78.9 - - - +
320C GLU* 1.3 61.6 + - + +
322C LYS* 3.1 36.8 - - - +
323C THR* 3.3 27.6 + - + +
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Residues in contact with GLU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C TYR* 2.4 31.6 + - + -
315C ARG 4.5 1.2 - - - +
316C ALA* 4.0 0.2 - - - -
317C THR* 3.1 36.7 + - - +
318C GLU 3.1 0.2 - - - -
319C GLU* 1.3 75.3 - - + +
321C PHE* 1.3 60.3 + - - +
322C LYS 3.1 1.3 - - - -
323C THR* 3.1 8.9 + - - +
324C TYR* 2.8 64.5 + - + +
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Residues in contact with PHE 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C TYR* 3.4 29.4 - + - +
310C TYR* 3.7 19.1 - + - -
311C SER* 3.5 43.1 - - - -
313C ASN 5.7 0.2 - - - -
316C ALA* 3.4 31.9 - - + -
317C THR 3.0 22.3 + - - -
318C GLU* 3.7 12.6 - - - +
320C GLU* 1.3 76.5 - - - +
322C LYS* 1.3 61.5 + - - +
324C TYR* 4.7 0.9 - - - -
325C SER* 2.5 30.4 + - - -
379C LYS* 3.4 29.7 - - + +
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Residues in contact with LYS 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C GLU* 2.9 15.2 + - + +
319C GLU* 3.1 40.8 - - - +
320C GLU 3.1 0.2 - - - -
321C PHE* 1.3 80.0 - - - +
323C THR* 1.3 81.4 + - - +
326C SER* 2.8 23.2 + - - -
379C LYS* 3.2 18.4 - - - +
380C VAL 6.0 0.2 - - - -
381C ASP* 3.0 42.2 + - - +
414C LYS* 3.5 18.1 - - - +
416C TYR* 4.9 1.0 - - - -
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Residues in contact with THR 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C GLU* 3.3 17.8 + - + +
320C GLU* 3.1 14.1 + - - +
322C LYS* 1.3 101.4 - - - +
324C TYR* 1.3 69.3 + - - +
326C SER* 3.4 7.2 + - - -
327C THR* 3.0 30.8 + - - -
415C THR* 4.6 15.5 - - + +
416C TYR* 4.4 9.4 - - + -
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Residues in contact with TYR 324 (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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284C GLU* 5.3 3.9 + - - -
303C TRP* 3.8 28.7 - + + -
306C PHE* 3.6 33.5 - + - -
307C TYR* 3.9 21.1 - + + -
310C TYR* 3.7 32.2 - + - -
320C GLU* 2.8 49.4 + - + +
321C PHE 4.9 0.2 - - - -
323C THR* 1.3 77.2 - - - +
325C SER* 1.3 67.3 + - - +
327C THR* 3.1 5.6 + - - -
328C ILE* 3.0 29.1 + - - +
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Residues in contact with SER 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C TYR* 2.9 26.4 + - - -
321C PHE 2.5 24.7 + - - -
324C TYR* 1.3 77.0 - - - +
326C SER* 1.3 62.6 + - - +
328C ILE* 3.4 4.5 + - - +
329C PHE* 3.1 17.3 + - - +
376C ILE* 3.4 30.9 + - - +
379C LYS* 3.4 17.9 - - - +
380C VAL* 3.6 12.1 - - - +
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Residues in contact with SER 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C LYS 2.8 17.5 + - - -
323C THR 3.5 8.7 - - - -
325C SER* 1.3 75.3 - - - +
327C THR* 1.3 67.0 + - - +
329C PHE 3.1 1.4 + - - -
330C LEU* 2.9 21.1 + - - +
380C VAL* 4.4 4.0 - - - +
381C ASP* 3.1 29.5 + - - -
384C LEU* 3.1 17.8 - - - +
416C TYR* 3.4 30.7 - - - -
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Residues in contact with THR 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C TRP* 3.6 38.5 - - + +
323C THR* 3.0 14.7 + - - -
324C TYR* 3.1 11.2 + - - -
326C SER* 1.3 75.3 - - - +
328C ILE* 1.3 64.3 + - - +
330C LEU* 3.3 2.1 + - - +
331C SER* 2.9 23.6 + - - -
416C TYR* 3.3 29.5 - - - +
419C GLN* 5.0 3.0 + - - +
420C TYR* 3.7 24.6 + - + +
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Residues in contact with ILE 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C THR* 3.8 6.2 - - + +
303C TRP* 3.7 35.2 - - + +
304C LYS* 3.9 18.8 - - + -
307C TYR* 3.6 38.6 - - + -
324C TYR 3.0 13.7 + - - +
325C SER* 3.7 7.2 - - - +
327C THR* 1.3 76.7 - - - +
329C PHE* 1.3 63.4 + - - +
331C SER* 3.1 19.3 + - - -
332C ALA* 3.3 9.9 + - - +
370C ILE* 3.6 27.3 - - + +
376C ILE* 4.5 11.4 - - + -
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Residues in contact with PHE 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C SER 3.1 16.5 + - - +
326C SER 3.7 3.1 - - - +
328C ILE* 1.3 73.4 - - - +
330C LEU* 1.3 65.7 + - - +
332C ALA* 3.1 12.3 + - - +
333C ILE* 3.1 28.3 + - + +
367C LEU* 3.6 21.1 - - + -
370C ILE* 3.8 22.6 - - + +
371C ILE* 3.8 19.7 - - + -
377C TYR* 3.9 16.2 - + - -
380C VAL* 4.1 18.6 - - + -
384C LEU* 3.3 43.7 - - + -
385C LYS* 4.3 3.8 - - - -
388C TYR* 3.5 29.2 - + + -
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Residues in contact with LEU 330 (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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326C SER 2.9 16.3 + - - +
327C THR* 3.8 3.4 - - - +
329C PHE* 1.3 77.9 - - - +
331C SER* 1.3 56.9 + - - +
333C ILE* 3.2 7.5 + - + +
334C SER* 2.8 32.7 + - - -
384C LEU* 4.0 14.5 - - + +
387C LEU* 4.0 26.2 - - + -
416C TYR* 3.6 28.0 - - + -
417C PHE* 3.7 28.5 - - + -
420C TYR* 3.9 26.7 - - + -
424C LEU* 4.3 16.8 - - + -
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Residues in contact with SER 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C PRO* 4.8 3.5 - - - +
299C HIS* 4.0 9.8 - - - -
300C THR* 3.1 22.8 + - - +
303C TRP* 5.5 1.4 - - - -
327C THR* 2.9 15.6 + - - -
328C ILE* 3.1 16.6 + - - -
330C LEU* 1.3 77.1 - - - +
332C ALA* 1.3 51.0 + - - +
334C SER* 3.8 4.9 - - - -
335C THR* 2.7 29.8 + - - -
420C TYR* 3.4 37.0 - - - -
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Residues in contact with ALA 332 (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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297C LEU* 6.3 0.2 - - - -
300C THR* 4.3 4.0 - - + -
328C ILE 3.3 1.5 + - - +
329C PHE 3.1 9.1 + - - +
330C LEU 3.1 1.0 - - - -
331C SER* 1.3 79.5 + - - +
333C ILE* 1.3 62.7 + - - +
334C SER 3.2 1.3 - - - -
335C THR* 3.6 17.2 + - - -
363C ARG* 3.7 14.4 + - - +
366C MET* 4.3 14.1 - - + -
367C LEU* 3.6 19.8 - - + +
370C ILE* 3.6 30.7 - - + -
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Residues in contact with ILE 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C PHE* 3.1 43.0 + - + +
330C LEU* 3.7 8.7 - - - +
332C ALA* 1.3 75.9 - - - +
334C SER* 1.3 58.3 + - - +
335C THR 3.1 5.7 + - - -
363C ARG* 2.8 29.8 + - - +
367C LEU* 3.9 14.8 - - + -
384C LEU* 4.1 4.7 - - + +
387C LEU* 3.8 27.8 - - + -
388C TYR* 4.3 13.2 - - + -
391C ILE* 4.7 13.7 - - + -
392C GLU* 4.9 5.2 - - + +
424C LEU* 4.2 17.3 - - + -
427C VAL* 3.7 11.9 - - + +
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Residues in contact with SER 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C PRO* 5.7 0.2 - - - +
330C LEU* 2.8 20.3 + - - -
331C SER* 3.9 10.8 - - - -
332C ALA 3.2 0.2 - - - -
333C ILE* 1.3 76.4 - - - +
335C THR* 1.3 61.8 + - - +
336C GLN 3.7 1.6 + - - -
420C TYR* 3.6 18.7 + - - -
423C PRO* 3.0 44.0 - - - +
424C LEU* 3.3 22.6 + - - +
427C VAL* 3.9 2.0 - - - -
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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