Contacts of the helix formed by residues 307 - 317 (chain w) in PDB entry 6AH0
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 SER 307 (chain w).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303w LYS 4.2 7.0 + - - -
304w ASN* 3.4 13.5 + - - +
306w LYS* 1.3 82.5 - - - +
308w LYS* 1.3 66.2 + - - +
309w GLY 3.2 3.9 + - - +
310w THR* 3.4 3.4 + - - +
311w LYS* 3.0 19.9 + - - -
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Residues in contact with LYS 308 (chain w).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306w LYS 3.8 1.0 + - - -
307w SER* 1.3 72.1 - - - +
309w GLY* 1.3 56.5 + - - +
311w LYS* 3.8 1.7 - - - +
312w ARG* 2.9 26.5 + - - -
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Residues in contact with GLY 309 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307w SER 3.2 1.0 - - - -
308w LYS* 1.3 74.4 - - - +
310w THR* 1.3 58.0 + - - +
312w ARG* 3.0 4.3 + - - -
313w ASP* 2.9 25.1 + - - -
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Residues in contact with THR 310 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290w GLY 6.4 2.0 - - - -
291w LYS* 6.5 1.3 - - - +
304w ASN 4.5 13.8 + - - -
305w PRO* 5.6 4.5 - - - -
307w SER* 3.4 5.9 + - - +
309w GLY* 1.3 76.0 - - - +
311w LYS* 1.3 57.4 + - - +
313w ASP* 4.5 1.3 - - - +
314w THR* 2.9 28.2 + - - -
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Residues in contact with LYS 311 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305w PRO 5.4 3.2 + - - -
306w LYS 5.4 0.9 - - - -
307w SER 3.0 15.1 + - - -
308w LYS* 3.8 3.4 - - - +
310w THR* 1.3 73.2 - - - +
312w ARG* 1.3 64.8 + - - +
314w THR* 3.8 0.6 - - - +
315w GLU* 2.9 21.8 + - - -
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Residues in contact with ARG 312 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308w LYS 2.9 15.7 + - - -
309w GLY 3.5 3.4 - - - -
311w LYS* 1.3 74.8 - - - +
313w ASP* 1.3 56.7 + - - +
315w GLU* 3.0 5.2 + - - +
316w ARG* 2.9 24.8 + - - -
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Residues in contact with ASP 313 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290w GLY* 4.2 25.9 - - - -
309w GLY 2.9 14.0 + - - -
310w THR* 4.0 1.6 - - - +
312w ARG* 1.3 69.8 - - - +
314w THR* 1.3 55.0 + - - +
315w GLU 2.9 4.5 - - - -
316w ARG* 2.9 2.2 + - - +
317w ASN* 2.7 34.8 + - - +
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Residues in contact with THR 314 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290w GLY* 4.8 5.8 - - - -
310w THR 2.9 20.2 + - - -
311w LYS* 3.8 1.3 - - - +
313w ASP* 1.3 71.4 - - - +
315w GLU* 1.3 58.0 + - - +
316w ARG 3.4 0.4 + - - -
317w ASN 5.3 0.4 - - - -
318w LYS* 3.9 18.9 - - - +
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Residues in contact with GLU 315 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311w LYS 2.9 14.0 + - - -
312w ARG 3.4 6.1 - - - -
313w ASP 2.9 1.0 - - - -
314w THR* 1.3 79.3 - - - +
316w ARG* 1.3 57.7 + - - +
318w LYS 4.8 0.9 - - - -
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Residues in contact with ARG 316 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312w ARG 2.9 10.7 + - - -
313w ASP* 3.6 1.3 - - - +
315w GLU* 1.3 79.7 - - - +
317w ASN* 1.3 56.4 + - - +
318w LYS 3.4 5.9 + - - -
319w ASP 5.0 1.6 + - - -
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Residues in contact with ASN 317 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289w LYS 5.5 1.4 - - - -
290w GLY* 5.3 10.8 + - - -
313w ASP* 2.7 18.5 + - - +
314w THR* 5.3 0.4 - - - -
316w ARG* 1.3 71.6 - - - +
318w LYS* 1.3 61.7 + - - +
319w ASP 3.5 1.6 - - - -
320w ILE* 3.6 5.5 + - - +
321w ALA* 3.0 21.5 + - - -
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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