Contacts of the helix formed by residues 314 - 332 (chain L) 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 GLY 314 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217L PRO* 4.8 5.1 - - - -
218L ASN* 4.7 15.9 - - - +
311L SER 2.7 13.4 + - - -
312L THR 3.4 1.4 - - - -
313L GLU* 1.3 80.5 - - - +
315L LYS* 1.3 65.4 + - - +
316L VAL 3.2 2.7 - - - -
317L GLY* 2.9 6.6 + - - -
318L TYR* 2.8 22.2 + - - -
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Residues in contact with LYS 315 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311L SER* 4.1 5.2 + - - +
313L GLU 3.4 4.2 + - - +
314L GLY* 1.3 77.2 - - - +
316L VAL* 1.3 50.7 + - - +
318L TYR* 3.1 1.8 + - - +
319L GLU* 2.8 32.1 + - - -
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Residues in contact with VAL 316 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302L ALA* 6.5 0.9 - - - -
311L SER* 5.2 6.6 + - - +
314L GLY 3.2 0.6 - - - -
315L LYS* 1.3 70.8 - - - +
317L GLY* 1.3 66.2 + - - +
319L GLU* 3.2 1.9 + - - +
320L LEU* 2.8 23.4 + - - -
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Residues in contact with GLY 317 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218L ASN* 3.8 32.3 - - - +
221L ILE* 5.3 5.4 - - - -
222L ILE* 5.2 7.0 + - - -
302L ALA* 6.1 3.3 - - - +
314L GLY* 2.9 9.3 + - - -
316L VAL* 1.3 74.6 - - - +
318L TYR* 1.3 57.7 + - - +
320L LEU* 3.5 1.6 + - - -
321L LYS* 2.8 25.6 + - - -
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Residues in contact with TYR 318 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314L GLY 2.8 16.7 + - - -
315L LYS 3.5 3.6 - - - -
317L GLY* 1.3 70.6 - - - +
319L GLU* 1.3 66.1 + - - +
321L LYS* 3.1 2.0 + - - +
322L ASP* 3.0 20.6 + - - -
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Residues in contact with GLU 319 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315L LYS 2.8 17.1 + - - -
316L VAL* 3.2 2.9 + - - +
318L TYR* 1.3 71.8 - - - +
320L LEU* 1.3 58.3 + - - +
322L ASP* 3.1 0.7 + - - -
323L GLU* 2.8 28.2 + - - -
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Residues in contact with LEU 320 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298L LYS* 6.5 1.1 - - - +
316L VAL 2.8 15.5 + - - -
317L GLY 3.7 1.6 - - - -
319L GLU* 1.3 75.1 - - - +
321L LYS* 1.3 62.6 + - - +
323L GLU* 3.4 2.2 + - - +
324L ILE* 2.9 19.6 + - - -
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Residues in contact with LYS 321 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221L ILE 6.0 0.7 - - - -
222L ILE* 5.6 8.7 - - - +
317L GLY 2.8 18.5 + - - -
318L TYR* 3.1 4.1 + - - +
320L LEU* 1.3 72.2 - - - +
322L ASP* 1.3 52.4 + - - +
324L ILE* 2.9 5.3 + - - +
325L GLU* 2.7 31.4 + - - -
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Residues in contact with ASP 322 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318L TYR 3.0 12.8 + - - -
319L GLU 3.7 2.5 - - - -
321L LYS* 1.3 71.4 - - - +
323L GLU* 1.3 56.6 + - - +
325L GLU* 3.1 2.5 + - - +
326L ARG* 2.8 33.1 + - - -
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Residues in contact with GLU 323 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319L GLU 2.8 15.7 + - - -
320L LEU* 3.7 3.1 - - - +
322L ASP* 1.3 78.1 - - - +
324L ILE* 1.3 58.4 + - - +
326L ARG* 3.7 1.5 + - - +
327L LYS* 3.6 14.2 + - - -
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Residues in contact with ILE 324 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320L LEU 2.9 11.0 + - - -
321L LYS* 2.9 8.6 + - - +
323L GLU* 1.3 74.4 - - - +
325L GLU* 1.3 64.1 + - - +
327L LYS* 3.6 2.0 + - - +
328L PHE* 3.2 16.3 + - - -
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Residues in contact with GLU 325 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321L LYS 2.7 13.7 + - - -
322L ASP* 3.1 4.4 + - - +
324L ILE* 1.3 75.6 - - - +
326L ARG* 1.3 59.9 + - - +
328L PHE* 3.0 3.9 + - - +
329L ASP* 2.9 24.6 + - - -
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Residues in contact with ARG 326 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322L ASP 2.8 15.9 + - - -
323L GLU* 3.7 2.7 + - - +
325L GLU* 1.3 78.0 - - - +
327L LYS* 1.3 56.1 + - - +
329L ASP* 3.1 4.3 + - - +
330L LYS* 2.9 23.2 + - - -
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Residues in contact with LYS 327 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323L GLU 3.6 12.3 + - - -
324L ILE 3.6 3.3 + - - -
325L GLU 3.3 0.6 - - - -
326L ARG* 1.3 73.3 - - - +
328L PHE* 1.3 65.8 + - - +
330L LYS* 3.3 2.9 + - - +
331L TRP* 3.1 19.4 + - - -
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Residues in contact with PHE 328 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324L ILE 3.2 11.6 + - - -
325L GLU* 3.0 8.7 + - - +
327L LYS* 1.3 79.5 - - - +
329L ASP* 1.3 50.8 + - - +
331L TRP* 3.5 1.6 + - - -
332L GLN* 2.7 37.9 + - - +
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Residues in contact with ASP 329 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325L GLU 2.9 12.7 + - - -
326L ARG* 3.1 4.9 + - - +
328L PHE* 1.3 76.7 - - - +
330L LYS* 1.3 55.4 + - - +
332L GLN* 2.7 27.2 + - - +
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Residues in contact with LYS 330 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326L ARG 2.9 13.5 + - - -
327L LYS* 3.3 4.9 + - - +
329L ASP* 1.3 76.5 - - - +
331L TRP* 1.3 61.2 + - - +
332L GLN* 4.2 0.2 - - - -
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Residues in contact with TRP 331 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327L LYS 3.1 12.9 + - - -
328L PHE* 3.7 2.7 - - - +
330L LYS* 1.3 73.8 - - - +
332L GLN* 1.3 63.4 + - - +
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Residues in contact with GLN 332 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328L PHE 2.7 15.2 + - - +
329L ASP* 2.7 22.2 + - - +
330L LYS 4.2 0.4 - - - -
331L TRP* 1.3 81.6 - - - +
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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