Contacts of the helix formed by residues 322 - 333 (chain C) in PDB entry 1YCH
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 VAL 322 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260C ASP* 4.4 15.3 - - + +
289C LEU* 3.9 20.0 - - + -
309C VAL* 3.9 27.6 - - + -
310C GLY 4.0 17.3 - - - +
311C SER* 4.1 13.0 - - - -
318C ILE* 4.5 5.2 - - + -
319C LEU* 3.1 20.6 + - + +
321C VAL* 1.3 78.9 - - - +
323C SER* 1.3 62.9 + - - +
324C PRO 3.5 0.2 - - - -
325C LEU* 3.6 6.0 + - + +
326C LEU* 3.4 28.1 + - + +
355C LEU* 4.3 6.5 - - + -
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Residues in contact with SER 323 (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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318C ILE* 3.6 16.1 - - - +
319C LEU 3.9 1.2 + - - -
320C PRO* 3.2 14.1 + - - +
322C VAL* 1.3 75.0 - - - +
324C PRO* 1.3 74.4 - - - +
326C LEU* 3.0 4.9 + - - +
327C ASP* 3.0 25.5 + - - +
358C ARG* 4.3 3.6 - - - +
323D SER* 3.6 21.1 - - - -
324D PRO 4.0 4.0 - - - -
327D ASP* 3.3 30.7 + - - +
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Residues in contact with PRO 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ARG* 3.9 20.2 - - + -
320C PRO 3.4 9.6 - - - +
321C VAL* 3.4 15.5 - - - +
323C SER* 1.3 93.0 - - - +
325C LEU* 1.3 60.6 + - - +
327C ASP* 3.5 0.3 + - - -
328C ASP* 3.0 26.2 + - - +
320D PRO* 3.6 27.7 - - + +
321D VAL* 5.3 1.8 - - - -
323D SER* 4.2 2.0 - - - +
324D PRO* 3.4 21.3 - - + -
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Residues in contact with LEU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C ALA* 4.2 14.4 - - + -
289C LEU* 4.1 21.1 - - + -
294C ARG* 4.2 14.2 - - + +
297C VAL* 4.0 21.5 - - + -
298C ILE* 3.8 28.9 - - + -
301C ILE* 4.5 5.2 - - + -
307C VAL* 5.6 0.4 - - + -
309C VAL* 4.1 31.6 - - + -
321C VAL 4.9 0.4 + - - -
322C VAL 3.6 8.4 + - - +
323C SER 3.3 0.8 - - - -
324C PRO* 1.3 77.7 - - - +
326C LEU* 1.3 59.1 + - + +
328C ASP* 3.5 3.8 + - - +
329C LEU* 3.0 45.0 + - + +
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Residues in contact with LEU 326 (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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309C VAL* 4.3 17.5 - - + -
318C ILE* 3.9 22.0 - - + -
322C VAL* 3.4 18.6 + - + +
323C SER 3.0 6.1 + - - +
325C LEU* 1.3 75.3 - - + +
327C ASP* 1.3 65.9 + - - +
328C ASP 3.0 1.8 - - - -
329C LEU* 3.1 8.2 + - + +
330C VAL* 3.1 27.9 + - - +
355C LEU* 3.9 25.4 - - + -
358C ARG* 4.0 39.8 - - + +
359C LEU* 4.2 24.0 - - + -
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Residues in contact with ASP 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C SER 3.0 8.7 + - - +
324C PRO* 4.2 2.5 - - + +
326C LEU* 1.3 76.0 - - - +
328C ASP* 1.3 61.1 + - - +
330C VAL* 3.6 5.1 + - - +
331C GLY* 3.3 8.7 + - - -
358C ARG* 3.3 20.6 + - - -
317D ASP* 3.2 46.3 - - - +
318D ILE* 4.6 4.0 - - + +
320D PRO* 4.9 7.1 - - + +
323D SER* 2.8 27.4 + - - +
354D ILE* 5.2 1.2 - - - +
358D ARG* 2.4 36.2 + - - -
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Residues in contact with ASP 328 (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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198C ASN* 4.5 2.4 - - - +
294C ARG* 3.0 31.8 + - - +
298C ILE* 3.3 31.6 - - + +
324C PRO 3.0 19.5 + - - +
325C LEU* 3.6 7.4 - - - +
327C ASP* 1.3 77.7 - - - +
329C LEU* 1.3 58.9 + - - +
330C VAL 3.4 0.2 - - - -
331C GLY* 4.0 1.2 - - - -
332C LEU* 3.0 50.1 + - - +
314D ILE* 6.1 1.2 - - - +
315D ASN* 5.5 2.3 + - - -
320D PRO* 3.5 10.3 - - + +
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Residues in contact with LEU 329 (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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201C MET* 5.6 1.1 - - - -
298C ILE* 4.0 11.9 - - + -
301C ILE* 3.9 28.0 - - + -
307C VAL* 4.6 5.8 - - + -
309C VAL* 5.1 0.4 - - + -
325C LEU* 3.0 41.2 + - + +
326C LEU* 3.1 8.5 + - + +
328C ASP* 1.3 76.5 - - - +
330C VAL* 1.3 65.0 + - - +
332C LEU* 4.6 2.2 - - + -
333C ARG 3.0 19.1 + - - -
334C PRO* 3.1 34.8 - - + +
358C ARG 5.9 0.2 - - - +
359C LEU* 4.5 12.3 - - + -
362C ALA* 3.6 11.0 - - + +
364C ILE* 4.1 19.1 - - + -
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Residues in contact with VAL 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 LEU 3.1 17.7 + - - +
327C ASP* 3.9 4.3 - - - +
329C LEU* 1.3 79.0 - - - +
331C GLY* 1.3 63.5 + - - +
333C ARG* 3.5 18.4 + - - +
358C ARG* 3.5 33.4 - - - +
361C ALA* 3.8 29.6 - - + +
362C ALA* 3.7 8.9 - - + +
317D ASP* 3.7 17.5 - - - +
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Residues in contact with GLY 331 (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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202C PRO* 4.0 7.4 - - - +
327C ASP 3.3 10.8 + - - -
328C ASP* 4.0 2.5 - - - -
329C LEU 3.2 0.4 - - - -
330C VAL* 1.3 82.7 - - - +
332C LEU* 1.3 58.9 + - - +
333C ARG* 3.2 11.6 + - - +
315D ASN* 3.5 41.4 - - - +
316D ASN* 5.2 0.7 + - - -
317D ASP* 3.8 6.7 + - - -
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Residues in contact with LEU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ALA 3.7 16.8 - - - +
198C ASN* 3.6 23.6 - - - +
199C ILE 5.0 0.4 - - - +
201C MET* 3.6 17.0 - - + +
202C PRO* 3.3 39.1 - - + -
298C ILE* 3.9 15.5 - - + -
328C ASP* 3.0 45.0 + - - +
329C LEU* 3.3 4.9 + - + +
331C GLY* 1.3 73.5 - - - +
333C ARG* 1.3 70.4 + - - +
334C PRO* 3.4 1.7 - - + -
315D ASN* 3.3 27.4 - - - +
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Residues in contact with ARG 333 (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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201C MET 4.3 7.1 - - - +
202C PRO* 4.6 17.2 - - + +
329C LEU 3.0 8.9 + - - -
330C VAL 3.6 13.7 + - - +
331C GLY 3.2 7.4 + - - +
332C LEU* 1.3 79.9 - - - +
334C PRO* 1.3 71.5 - - - +
335C LYS* 3.3 5.2 + - - +
361C ALA 5.9 1.1 - - - +
362C ALA 4.4 7.6 - - - +
363C LYS* 5.8 8.1 - - + -
316D ASN* 3.7 26.8 - - - +
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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