Contacts of the helix formed by residues 306 - 316 (chain A) in PDB entry 6R7Y
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 PRO 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A VAL* 6.0 3.8 - - + -
304A LEU 4.6 1.8 - - - +
305A TYR* 1.3 115.0 - - + +
307A SER* 1.3 65.8 + - - +
308A TYR* 3.3 36.6 + - + +
309A LYS* 3.3 20.6 + - + +
310A ARG 3.6 0.7 + - - -
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Residues in contact with SER 307 (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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305A TYR 3.5 3.7 + - - -
306A PRO* 1.3 72.5 - - - +
308A TYR* 1.3 59.8 + - - +
310A ARG* 3.3 21.5 + - - +
311A GLN* 3.0 40.2 + - - +
618B ARG* 5.0 10.4 + - - -
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Residues in contact with TYR 308 (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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306A PRO* 3.6 27.2 - - + +
307A SER* 1.3 78.1 - - - +
309A LYS* 1.3 94.6 + - + +
311A GLN* 3.8 6.6 - - - +
312A LEU* 2.9 41.8 + - + +
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Residues in contact with LYS 309 (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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305A TYR* 3.6 32.3 - - + +
306A PRO* 3.3 17.8 + - + +
307A SER 3.3 0.6 - - - -
308A TYR* 1.3 103.7 - - + +
310A ARG* 1.3 60.1 + - - +
312A LEU* 3.8 7.3 - - + +
313A ARG* 3.0 35.3 + - - +
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Residues in contact with ARG 310 (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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288A PHE* 4.4 5.5 - - - -
305A TYR* 3.8 38.0 + - + +
306A PRO 3.6 3.0 + - - +
307A SER* 3.3 23.6 + - - +
308A TYR 3.3 0.4 - - - -
309A LYS* 1.3 79.3 - - - +
311A GLN* 1.3 70.2 + - - +
313A ARG* 3.4 5.7 + - - +
314A ILE* 3.1 35.2 + - + +
388A GLU 3.9 12.3 - - - +
389A ASN 3.1 27.5 + - - -
390A HIS* 3.9 20.9 + - - -
391A ARG* 4.5 18.7 - - - +
618B ARG* 5.6 5.7 - - - +
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Residues in contact with GLN 311 (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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307A SER* 3.0 31.6 + - - +
308A TYR* 3.9 7.2 - - - +
310A ARG* 1.3 85.8 - - - +
312A LEU* 1.3 59.3 + - + +
314A ILE* 3.9 10.4 - - - +
315A TYR* 3.0 59.4 + - + +
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Residues in contact with LEU 312 (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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308A TYR* 2.9 30.6 + - + +
309A LYS* 3.8 8.1 - - + +
310A ARG 3.3 0.2 - - - -
311A GLN* 1.3 76.2 - - + +
313A ARG* 1.3 60.5 + - + +
315A TYR* 4.6 1.6 - - + +
316A LEU* 2.9 62.2 + - + +
317A VAL* 4.0 1.3 + - - +
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Residues in contact with ARG 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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289A HIS* 5.3 6.9 - - - -
305A TYR* 2.7 37.4 + - - -
309A LYS* 3.0 23.7 + - - +
310A ARG* 3.4 5.6 + - - +
312A LEU* 1.3 76.4 - - + +
314A ILE* 1.3 54.2 + - - +
317A VAL* 3.7 12.3 - - + +
318A SER* 2.6 29.5 + - - -
387A TRP* 3.3 76.1 + - + +
388A GLU* 4.6 14.1 - - + +
389A ASN* 4.9 8.1 - - - +
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Residues in contact with ILE 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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310A ARG* 3.1 22.5 + - + +
311A GLN* 3.9 12.8 - - - +
312A LEU 3.2 0.2 - - - -
313A ARG* 1.3 76.0 - - - +
315A TYR* 1.3 83.6 + - + +
316A LEU 3.1 5.7 + - - -
318A SER* 3.2 15.8 + - - +
319A LEU* 3.1 28.0 + - + +
388A GLU* 3.7 21.5 - - + +
390A HIS* 3.8 28.3 - - + -
399A HIS* 4.0 23.1 - - + +
403A LYS* 5.1 5.6 - - - +
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Residues in contact with TYR 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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311A GLN* 3.0 38.2 + - + +
312A LEU* 5.4 1.1 - - + -
314A ILE* 1.3 94.4 - - + +
316A LEU* 1.3 71.5 + - + +
319A LEU* 4.0 29.4 - - + +
320A PRO* 4.3 8.3 - - - +
399A HIS* 5.9 4.0 - + - -
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Residues in contact with LEU 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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312A LEU* 2.9 41.2 + - + +
315A TYR* 1.3 88.1 - - + +
317A VAL* 1.3 66.5 + - + +
320A PRO* 3.3 22.8 - - + +
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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