Contacts of the helix formed by residues 312 - 317 (chain A) in PDB entry 5YDJ
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 ALA 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A VAL 4.9 1.1 - - - +
281A PHE 2.8 22.6 + - - -
282A TYR* 3.9 19.1 - - + +
311A VAL* 1.3 75.9 - - + +
313A SER* 1.3 64.0 + - - +
315A GLY 3.2 1.6 + - - -
316A PHE* 3.0 29.5 + - - +
437A VAL* 4.0 15.9 - - + -
440A GLU* 3.3 22.0 - - - +
451A PHE* 3.9 8.1 - - - -
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Residues in contact with SER 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PHE* 3.5 6.0 - - - -
312A ALA* 1.3 76.6 - - - +
314A LEU* 1.3 66.9 + - - +
317A LEU* 3.1 32.9 + - - +
408A LEU* 3.7 30.0 - - - +
436A LEU* 4.5 8.7 + - - +
437A VAL* 4.4 6.9 - - - +
440A GLU* 2.7 24.5 + - - +
451A PHE* 3.7 22.4 - - - +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ARG* 3.6 26.1 - - + +
206A PHE* 4.1 17.7 + - + -
229A VAL* 3.7 39.9 - - + +
253A GLU* 3.5 23.6 - - + +
310A ARG* 3.6 32.4 + - + -
311A VAL 3.7 9.0 - - - +
312A ALA* 3.2 0.6 - - - +
313A SER* 1.3 81.6 + - - +
315A GLY* 1.3 54.9 + - - +
328A ALA* 4.8 0.2 - - - +
433A PRO* 3.8 15.3 - - + +
436A LEU* 3.9 18.6 - - + -
437A VAL* 4.3 9.2 - - + -
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Residues in contact with GLY 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PHE* 5.8 0.4 - - - -
310A ARG* 3.6 28.2 - - - +
311A VAL 3.4 5.5 + - - -
312A ALA 3.2 5.1 + - - -
314A LEU* 1.3 79.4 - - - +
316A PHE* 1.3 63.7 + - - +
317A LEU 4.0 0.7 - - - -
328A ALA* 3.0 16.7 + - - -
329A GLY 2.7 25.5 + - - -
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Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A PHE* 3.4 39.5 - + + -
309A TYR* 4.5 4.5 - + - -
310A ARG 3.6 18.6 - - - -
311A VAL* 4.5 1.8 - - - -
312A ALA 3.0 16.8 + - - +
313A SER 3.9 0.9 - - - -
315A GLY* 1.3 84.2 - - - +
317A LEU* 1.3 65.0 + - - +
318A PHE* 3.6 5.4 + - - +
326A GLY* 5.1 2.4 - - - -
327A ASN* 4.0 15.7 - - - +
329A GLY* 3.7 15.7 - - - -
330A LEU* 4.0 19.5 - - + -
401A ALA* 5.9 0.7 - - - +
451A PHE* 3.7 31.4 - - - +
452A VAL 3.6 18.9 - - - +
453A PRO* 3.6 32.8 - - + -
454A VAL* 5.8 1.0 - - - +
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PHE* 3.5 42.5 + - + +
313A SER* 3.1 19.6 + - - +
315A GLY 4.0 0.8 - - - -
316A PHE* 1.3 77.7 - - - +
318A PHE* 1.3 59.8 + - - +
319A LEU* 4.6 3.4 - - + -
324A ALA* 3.9 23.1 - - + +
326A GLY* 3.5 19.6 + - - -
405A ALA* 3.7 25.4 - - + -
408A LEU* 3.7 30.3 - - + -
425A VAL* 5.0 1.3 - - + -
428A LEU* 3.9 18.4 - - + -
451A PHE* 3.7 13.0 - - + -
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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