Contacts of the helix formed by residues 397 - 413 (chain C) in PDB entry 5YDI
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 397 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C VAL* 1.3 73.6 - - - +
398C ARG* 1.3 54.2 + - - +
399C GLU* 4.5 6.8 + - - +
400C GLU* 3.1 24.6 + - - +
401C ALA* 2.7 31.6 + - - +
455C VAL* 6.1 1.8 - - - -
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Residues in contact with ARG 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLY 3.5 18.3 + - - -
321A THR* 5.0 1.1 - - - -
322A PRO* 3.1 39.3 - - - +
318C PHE* 3.4 34.3 - - + -
320C GLY* 4.7 7.9 + - - -
396C VAL 3.5 1.2 + - - -
397C SER* 1.3 72.8 - - - +
399C GLU* 1.3 62.6 + - - +
401C ALA* 3.1 1.6 + - - +
402C THR* 2.9 31.8 + - - +
454C VAL* 3.8 17.3 - - + -
455C VAL* 3.3 37.8 + - + +
456C ASP 3.6 13.0 + - - -
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Residues in contact with GLU 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C SER* 3.3 6.8 + - - +
398C ARG* 1.3 77.9 - - - +
400C GLU* 1.3 57.5 + - - +
402C THR* 2.7 19.8 + - - -
403C LEU* 3.2 25.2 - - + +
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Residues in contact with GLU 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C VAL* 5.1 3.4 - - + -
397C SER* 3.0 23.4 + - - +
399C GLU* 1.3 77.2 + - - +
401C ALA* 1.3 57.3 + - - +
402C THR 3.1 2.0 - - - -
403C LEU* 2.7 35.6 + - - +
404C ARG* 2.8 55.2 + - - +
407C ARG* 3.5 22.7 + - - -
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Residues in contact with ALA 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C PHE* 3.4 32.1 + - + +
396C VAL* 3.8 22.4 - - + +
397C SER 2.7 19.8 + - - +
398C ARG* 3.1 7.6 + - - +
400C GLU* 1.3 72.3 - - - +
402C THR* 1.3 61.6 + - - +
404C ARG* 3.4 13.2 + - - +
405C ALA* 3.1 18.4 + - - +
451C PHE* 4.8 4.2 - - + -
454C VAL* 4.3 3.4 - - + -
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Residues in contact with THR 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C PHE* 3.6 15.5 - - + -
319C LEU* 3.6 36.4 - - - +
320C GLY* 5.2 0.2 - - - -
398C ARG 2.9 16.4 + - - +
399C GLU* 2.7 27.9 + - - -
401C ALA* 1.3 76.1 - - - +
403C LEU* 1.3 62.9 + - - +
405C ALA* 3.4 3.0 + - - +
406C LEU* 3.0 37.9 + - - +
421C LEU* 5.9 2.7 - - + -
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Residues in contact with LEU 403 (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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399C GLU* 3.2 27.4 - - + +
400C GLU* 2.7 30.9 + - - +
402C THR* 1.3 80.0 + - - +
404C ARG* 1.3 57.5 + - - +
406C LEU* 3.3 13.8 + - + +
407C ARG* 2.9 54.3 + - - +
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Residues in contact with ARG 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C VAL* 3.4 29.9 - - - +
400C GLU* 2.8 49.6 + - - +
401C ALA* 3.6 9.6 - - - +
402C THR 3.4 0.2 - - - -
403C LEU* 1.3 74.8 - - - +
405C ALA* 1.3 58.3 + - - +
407C ARG* 3.3 21.6 + - - +
408C LEU* 3.0 28.1 + - - +
444C LEU* 4.6 16.8 - - - +
448C GLU* 5.9 4.8 + - - +
449C PHE 3.5 7.5 + - - -
450C PRO* 2.5 49.0 + - + +
451C PHE* 3.7 22.2 - - + -
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Residues in contact with ALA 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C LEU* 3.7 19.5 - - + -
318C PHE 3.5 25.8 - - - +
319C LEU* 3.6 23.3 - - + -
401C ALA 3.1 3.8 + - - +
402C THR 3.5 7.2 - - - +
403C LEU 3.2 0.2 - - - -
404C ARG* 1.3 80.8 - - - +
406C LEU* 1.3 56.8 + - - +
408C LEU* 3.4 4.3 + - - +
409C ALA* 3.1 23.4 + - - +
428C LEU* 4.3 8.0 - - - +
451C PHE* 3.9 4.9 - - + -
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Residues in contact with LEU 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C LEU* 4.3 10.5 - - + -
402C THR* 3.0 26.8 + - - +
403C LEU* 3.3 14.3 + - + +
405C ALA* 1.3 73.7 - - - +
407C ARG* 1.3 60.6 + - - +
409C ALA* 3.3 6.1 + - + +
410C GLU* 3.0 23.0 + - - +
416C HIS* 3.4 40.0 - - + +
417C GLU 4.4 1.8 - - - +
418C PRO* 4.0 27.8 - - + -
421C LEU* 3.9 26.0 - - + -
424C ALA* 4.5 9.9 - - + -
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Residues in contact with ARG 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C GLU* 3.5 30.6 + - - -
403C LEU* 2.9 39.7 + - - +
404C ARG* 3.3 21.7 + - - +
406C LEU* 1.3 73.2 - - - +
408C LEU* 1.3 54.7 + - - +
410C GLU* 3.3 13.6 + - - +
411C ALA* 2.7 37.7 + - - +
439C ASN 5.8 0.2 - - - -
443C THR 5.8 1.6 + - - -
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Residues in contact with LEU 408 (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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206C PHE* 5.9 0.2 - - + -
313C SER* 3.8 31.9 - - - +
317C LEU* 4.1 11.7 - - + -
404C ARG 3.0 13.8 + - - +
405C ALA 3.5 8.7 - - - +
407C ARG* 1.3 74.1 - - - +
409C ALA* 1.3 59.8 + - - +
411C ALA* 3.8 4.0 - - - +
412C VAL* 2.9 35.8 + - + +
428C LEU* 4.3 11.2 - - + -
436C LEU* 3.4 37.7 - - + +
439C ASN* 3.9 29.2 - - + +
440C GLU* 4.3 3.4 - - - +
451C PHE* 4.0 13.9 - - + -
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Residues in contact with ALA 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C ALA 3.1 13.8 + - - +
406C LEU* 3.3 14.1 + - - +
408C LEU* 1.3 76.9 - - - +
410C GLU* 1.3 54.0 + - - +
412C VAL* 3.5 0.9 - - - +
413C GLY 3.0 9.9 + - - -
414C CYS* 2.7 37.2 + - + +
415C PRO 3.8 21.8 - - - +
416C HIS* 4.4 2.0 - - + -
424C ALA* 4.6 7.4 - - + -
428C LEU* 3.8 20.4 - - + +
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Residues in contact with GLU 410 (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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406C LEU 3.0 11.7 + - - +
407C ARG* 3.7 14.8 - - - +
409C ALA* 1.3 75.0 - - - +
411C ALA* 1.3 65.4 + - - +
413C GLY* 3.0 14.2 + - - -
414C CYS 4.0 0.4 - - - -
416C HIS* 3.5 45.1 + - + +
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Residues in contact with ALA 411 (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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407C ARG 2.7 23.3 + - - +
408C LEU* 3.8 4.9 - - - +
410C GLU* 1.3 74.5 - - - +
412C VAL* 1.3 58.8 + - - +
413C GLY 3.6 0.2 + - - -
439C ASN* 3.4 36.8 + - + +
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Residues in contact with VAL 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C LEU* 2.9 25.8 + - + +
409C ALA 3.5 7.6 - - - +
411C ALA* 1.3 75.9 - - - +
413C GLY* 1.3 58.9 + - - +
414C CYS* 4.2 10.8 - - - -
428C LEU* 3.8 21.8 - - + -
431C LYS* 3.8 26.4 + - + -
435C VAL* 4.0 37.7 - - + +
436C LEU* 4.2 15.5 - - + -
439C ASN* 4.3 5.4 - - - +
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Residues in contact with GLY 413 (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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409C ALA 3.0 2.2 + - - -
410C GLU* 3.0 12.2 + - - -
411C ALA 3.3 0.6 + - - -
412C VAL* 1.3 81.1 - - - +
414C CYS* 1.3 65.4 + - - +
415C PRO* 4.9 0.2 - - - +
416C HIS* 6.1 0.7 - - - -
427C CYS* 4.3 1.7 - - - -
431C LYS* 3.9 10.1 + - - -
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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
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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