Contacts of the helix formed by residues 311 - 317 (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 VAL 311 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228C CYS* 4.5 11.1 - - + +
229C VAL 3.9 18.8 - - - +
230C GLN* 4.1 7.4 - - + +
277C PHE* 5.1 1.6 - - + -
281C PHE* 3.4 29.2 - - - -
282C TYR 3.7 16.4 - - - +
283C SER* 3.4 26.2 - - - +
284C GLY 5.3 0.9 - - - +
309C TYR* 3.5 20.4 + - + +
310C ARG* 1.3 74.6 - - - +
312C ALA* 1.3 77.5 + - + +
314C LEU* 3.7 9.8 + - - +
315C GLY 3.2 9.5 + - - -
316C PHE* 4.3 2.9 - - + -
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Residues in contact with ALA 312 (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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229C VAL 4.7 0.2 - - - +
231C ILE* 4.9 0.2 - - + -
281C PHE 2.9 23.6 + - - -
282C TYR* 4.0 17.9 - - - +
311C VAL* 1.3 75.9 - - + +
313C SER* 1.3 58.3 + - - +
315C GLY 3.2 0.7 + - - -
316C PHE* 2.8 37.3 + - - +
437C VAL* 4.0 16.2 - - + -
440C GLU* 3.2 22.2 - - - +
451C PHE* 3.9 8.7 - - - -
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Residues in contact with SER 313 (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* 3.5 4.5 - - - -
312C ALA* 1.3 78.4 - - - +
314C LEU* 1.3 65.6 + - - +
317C LEU* 2.9 37.7 + - - +
408C LEU* 3.8 19.9 - - - +
436C LEU* 4.1 18.5 + - - +
437C VAL* 4.5 0.7 - - - +
440C GLU* 2.8 18.1 + - - -
451C PHE* 3.6 30.4 - - - -
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Residues in contact with LEU 314 (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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205C ARG* 4.0 17.3 - - + +
206C PHE* 3.8 21.0 + - + -
228C CYS* 6.2 0.7 - - + -
229C VAL* 3.5 47.3 - - + +
253C GLU* 3.9 23.1 - - + +
310C ARG* 3.8 29.9 + - + -
311C VAL 3.7 6.3 - - - +
312C ALA 3.3 0.6 - - - -
313C SER* 1.3 82.5 + - - +
315C GLY* 1.3 57.4 + - - +
328C ALA* 4.5 0.3 - - - +
433C PRO* 4.1 12.1 - - + +
436C LEU* 3.9 26.7 - - + -
437C VAL* 4.3 10.5 - - + -
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Residues in contact with GLY 315 (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* 6.3 0.2 - - - -
310C ARG* 3.6 32.3 - - - -
311C VAL 3.2 6.5 + - - -
312C ALA 3.2 4.7 + - - -
313C SER 3.1 0.2 - - - -
314C LEU* 1.3 78.6 - - - +
316C PHE* 1.3 62.6 + - - +
317C LEU 3.8 1.3 - - - -
328C ALA* 3.0 17.5 + - - +
329C GLY 2.8 22.0 + - - -
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Residues in contact with PHE 316 (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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281C PHE* 3.5 41.5 - + + -
309C TYR* 4.5 7.4 - + - -
310C ARG 3.6 17.7 - - - -
311C VAL* 4.3 4.3 - - - -
312C ALA 2.8 24.1 + - - +
313C SER 3.8 0.4 - - - -
315C GLY* 1.3 78.5 - - - +
317C LEU* 1.3 65.1 - - - +
318C PHE* 3.5 6.6 + - - +
326C GLY* 4.9 0.9 - - - -
327C ASN* 4.2 14.7 + - - +
329C GLY* 4.0 13.2 - - - -
330C LEU* 3.9 22.2 - - + -
451C PHE* 3.8 28.9 - - - +
452C VAL 3.7 11.9 - - - +
453C PRO* 3.6 36.1 - - + -
454C VAL* 5.5 1.2 - - - +
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Residues in contact with LEU 317 (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* 3.6 45.9 - - + +
313C SER* 2.9 21.2 + - - +
315C GLY 3.8 1.2 - - - -
316C PHE* 1.3 76.1 - - - +
318C PHE* 1.3 59.8 + - - +
319C LEU* 3.8 20.9 - - + -
324C ALA* 4.0 12.2 - - + +
326C GLY* 3.2 21.1 + - - -
328C ALA* 6.1 0.7 - - - +
405C ALA* 3.7 28.3 - - + -
408C LEU* 4.1 22.7 - - + -
425C VAL* 4.8 1.1 - - + -
428C LEU* 4.0 11.9 - - + -
451C PHE* 4.1 11.0 - - + -
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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
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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