Contacts of the helix formed by residues 311 - 317 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B CYS* 4.5 9.2 - - + +
229B VAL 3.9 20.0 - - - +
230B GLN* 4.0 12.1 - - + +
277B PHE* 4.9 3.1 - - + -
281B PHE* 3.4 17.0 - - - -
282B TYR 3.6 16.2 - - - +
283B SER* 3.4 36.3 - - - +
284B GLY 5.2 0.9 - - - +
309B TYR* 3.4 18.3 + - + +
310B ARG* 1.3 75.2 - - - +
312B ALA* 1.3 76.6 + - + +
314B LEU* 3.6 9.4 + - - +
315B GLY* 3.2 9.7 + - - -
316B PHE* 4.6 2.0 - - + -
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B VAL 4.9 0.7 - - - +
231B ILE* 4.9 0.4 - - + -
281B PHE 2.8 23.7 + - - -
282B TYR* 3.9 19.3 - - - +
311B VAL* 1.3 77.7 - - + +
313B SER* 1.3 54.9 + - - +
315B GLY 3.2 0.9 + - - -
316B PHE* 2.8 37.0 + - - +
437B VAL* 4.2 15.0 - - + -
440B GLU* 3.1 23.8 - - - +
450B PRO* 6.4 0.2 - - - -
451B PHE* 3.8 8.7 - - - -
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B PHE* 3.6 5.7 - - - -
312B ALA* 1.3 74.0 - - - +
314B LEU* 1.3 63.1 + - - +
316B PHE 4.3 0.2 - - - +
317B LEU* 3.0 35.4 + - - +
408B LEU* 3.8 18.4 - - - +
436B LEU* 4.1 15.9 + - - +
437B VAL* 4.4 1.4 - - - +
440B GLU* 2.8 27.6 + - - -
451B PHE* 3.6 32.5 - - - +
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ARG* 3.5 35.7 - - + +
206B PHE* 4.0 17.9 + - + -
229B VAL* 3.6 38.4 - - + +
253B GLU* 4.1 9.2 - - + +
310B ARG* 3.6 29.8 + - + -
311B VAL 3.6 6.0 + - - +
312B ALA 3.2 0.8 - - - -
313B SER* 1.3 83.0 + - - +
315B GLY* 1.3 57.8 + - - +
433B PRO* 4.1 9.4 - - + -
436B LEU* 3.9 23.1 - - + -
437B VAL* 3.8 22.7 - - + -
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Residues in contact with GLY 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B PHE* 6.0 0.4 - - - -
310B ARG* 3.5 33.4 - - - +
311B VAL 3.2 6.3 + - - -
312B ALA 3.2 5.6 + - - -
313B SER 3.1 0.4 - - - -
314B LEU* 1.3 79.7 - - - +
316B PHE* 1.3 62.2 + - - +
317B LEU 3.8 1.7 + - - +
328B ALA* 3.0 17.9 + - - +
329B GLY 2.9 21.1 + - - -
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B PHE* 3.6 39.0 - + + -
309B TYR* 4.5 6.7 - + - -
310B ARG 3.7 19.7 - - - -
311B VAL* 4.7 0.4 - - - -
312B ALA 2.8 22.2 + - - +
313B SER 3.9 0.4 - - - -
315B GLY* 1.3 77.0 - - - +
317B LEU* 1.3 64.3 - - - +
318B PHE* 3.5 5.9 + - - +
326B GLY* 4.7 1.7 - - - -
327B ASN* 3.8 28.6 + - - +
329B GLY* 3.9 10.5 - - - -
330B LEU* 3.7 29.4 - - + -
451B PHE* 4.0 29.2 - - - -
452B VAL 3.8 24.3 - - - +
453B PRO* 3.8 13.5 - - + -
454B VAL* 5.7 1.0 - - - +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B PHE* 3.8 34.5 - - + +
313B SER* 3.0 20.1 + - - +
315B GLY 3.8 1.2 - - - +
316B PHE* 1.3 75.3 - - - +
318B PHE* 1.3 61.7 + - - +
319B LEU* 4.1 13.2 - - + -
324B ALA* 3.7 29.5 - - + +
326B GLY* 3.2 21.2 + - - -
328B ALA* 6.0 0.5 - - - +
405B ALA* 3.8 23.8 - - + -
408B LEU* 4.1 19.7 - - + -
425B VAL* 4.5 2.0 - - + -
428B LEU* 4.3 15.3 - - + -
451B PHE* 3.9 18.6 - - + -
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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