Contacts of the helix formed by residues 334 - 350 (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 LEU 334 (chain w).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330w TYR 3.1 9.0 + - - -
331w VAL* 3.1 10.2 + - - +
332w GLU 3.0 1.0 - - - -
333w ILE* 1.3 79.1 - - - +
335w GLY* 1.3 64.2 + - - +
336w GLU 3.1 3.4 - - - -
337w GLN* 2.8 17.1 + - - +
338w ARG* 2.9 10.7 + - - -
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Residues in contact with GLY 335 (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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331w VAL 3.1 10.3 + - - -
332w GLU* 3.2 10.9 + - - -
333w ILE 3.5 1.6 + - - -
334w LEU* 1.3 76.2 - - - +
336w GLU* 1.3 55.7 + - - +
338w ARG* 3.3 2.5 + - - -
339w HIS* 2.9 26.9 + - - -
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Residues in contact with GLU 336 (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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333w ILE 5.4 0.2 + - - -
334w LEU 3.1 1.4 - - - -
335w GLY* 1.3 75.6 - - - +
337w GLN* 1.3 57.0 + - - +
339w HIS* 4.0 1.2 - - - +
340w LEU* 2.9 24.9 + - - -
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Residues in contact with GLN 337 (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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177w ARG 5.5 3.6 - - - -
178w LYS 4.5 14.7 - - - +
179w ASN* 5.0 2.6 - - - -
180w ALA 5.1 3.9 + - - -
334w LEU* 2.8 8.7 + - - +
336w GLU* 1.3 73.0 - - - +
338w ARG* 1.3 66.8 + - - +
340w LEU* 3.7 1.2 - - - +
341w THR* 2.9 21.3 + - - -
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Residues in contact with ARG 338 (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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334w LEU 2.9 11.7 + - - -
335w GLY* 3.7 4.0 - - - -
337w GLN* 1.3 76.2 - - - +
339w HIS* 1.3 61.6 + - - +
341w THR* 3.2 1.0 + - - -
342w HIS* 2.9 20.6 + - - -
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Residues in contact with HIS 339 (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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335w GLY 2.9 16.0 + - - -
336w GLU 4.0 1.1 - - - -
338w ARG* 1.3 73.3 - - - +
340w LEU* 1.3 62.9 + - - +
342w HIS* 3.2 2.3 + - - +
343w GLU* 2.9 21.5 + - - -
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Residues in contact with LEU 340 (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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178w LYS 5.2 6.1 - - - -
336w GLU 2.9 18.7 + - - -
337w GLN* 3.3 2.4 + - - +
339w HIS* 1.3 74.0 - - - +
341w THR* 1.3 58.2 + - - +
343w GLU* 3.4 1.8 + - - +
344w ASN* 3.0 22.3 + - - -
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Residues in contact with THR 341 (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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178w LYS 5.0 1.6 + - - -
179w ASN* 5.0 12.6 - - - +
180w ALA 5.4 5.2 - - - +
337w GLN 2.9 15.0 + - - -
338w ARG 3.7 2.7 - - - -
340w LEU* 1.3 72.9 - - - +
342w HIS* 1.3 66.3 + - - +
344w ASN* 2.7 14.4 + - - +
345w VAL* 2.8 11.6 + - - -
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Residues in contact with HIS 342 (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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338w ARG 2.9 14.8 + - - -
339w HIS* 3.7 2.9 - - - +
341w THR* 1.3 72.7 - - - +
343w GLU* 1.3 62.7 + - - +
345w VAL* 3.2 2.8 + - - +
346w GLN* 3.0 19.9 + - - -
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Residues in contact with GLU 343 (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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339w HIS 2.9 14.0 + - - -
340w LEU 3.7 4.3 - - - -
342w HIS* 1.3 74.9 - - - +
344w ASN* 1.3 63.7 + - - +
346w GLN* 3.0 3.9 + - - +
347w ARG* 2.9 20.1 + - - -
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Residues in contact with ASN 344 (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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340w LEU 3.0 11.3 + - - -
341w THR* 2.7 14.6 + - - +
343w GLU* 1.3 69.4 - - - +
345w VAL* 1.3 61.8 + - - +
347w ARG* 3.1 3.9 + - - +
348w LYS* 2.9 22.3 + - - -
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Residues in contact with VAL 345 (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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341w THR 2.8 15.0 + - - -
342w HIS* 3.6 4.3 - - - +
344w ASN* 1.3 71.3 - - - +
346w GLN* 1.3 63.1 + - - +
348w LYS* 3.9 0.7 - - - +
349w GLN* 2.9 22.2 + - - -
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Residues in contact with GLN 346 (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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342w HIS 3.0 13.3 + - - -
343w GLU 3.0 3.1 + - - -
345w VAL* 1.3 73.0 - - - +
347w ARG* 1.3 62.6 + - - +
349w GLN* 3.3 2.3 + - - +
350w ALA* 3.0 19.6 + - - -
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Residues in contact with ARG 347 (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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343w GLU 2.9 13.3 + - - -
344w ASN* 3.5 3.6 - - - +
346w GLN* 1.3 70.4 - - - +
348w LYS* 1.3 56.9 + - - +
350w ALA* 2.7 25.6 + - - -
351w ARG* 3.1 8.7 + - - -
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Residues in contact with LYS 348 (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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344w ASN 2.9 16.4 + - - -
345w VAL* 3.9 1.3 - - - +
347w ARG* 1.3 70.0 - - - +
349w GLN* 1.3 62.1 + - - +
351w ARG* 3.1 16.0 + - - +
352w THR 5.5 0.5 - - - +
356w ARG* 5.5 7.7 - - - +
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Residues in contact with GLN 349 (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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345w VAL 2.9 17.9 + - - -
346w GLN* 3.6 2.9 - - - +
347w ARG 2.9 0.2 + - - -
348w LYS* 1.3 76.3 - - - +
350w ALA* 1.3 57.2 + - - +
351w ARG 3.2 7.7 + - - +
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Residues in contact with ALA 350 (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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346w GLN 3.0 9.3 + - - -
347w ARG* 2.7 16.3 + - - +
349w GLN* 1.3 69.8 - - - +
351w ARG* 1.3 62.1 + - - +
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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