Contacts of the helix formed by residues 312 - 321 (chain D) in PDB entry 6B0Z
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 VAL 312 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D MET* 3.6 9.8 - - + +
19D THR* 5.3 3.1 - - - +
309D HIS* 4.1 5.6 - - + +
310D GLY 3.8 9.9 - - - +
311D THR* 1.3 75.7 + - - +
313D THR* 1.3 65.3 + - - +
314D ARG 3.1 2.9 - - - +
315D HIS* 3.1 52.8 + - + +
316D TYR 3.2 8.1 + - - -
327D THR* 4.2 12.1 - - + -
501D NDP 2.6 66.9 + - + +
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Residues in contact with THR 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLU* 2.7 38.8 + - - +
82D ARG* 3.0 17.9 + - - +
311D THR* 3.2 4.4 + - - -
312D VAL* 1.3 73.1 - - - +
314D ARG* 1.3 65.1 + - - +
316D TYR* 3.0 16.4 + - + +
317D ARG* 3.1 36.7 + - + +
501D NDP 3.6 16.4 + - - -
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Residues in contact with ARG 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D VAL 3.1 0.4 - - - -
313D THR* 1.3 80.3 - - - +
315D HIS* 1.3 79.2 + - + +
317D ARG* 3.7 6.4 + - - +
318D MET* 3.4 40.7 + - - +
501D NDP 3.0 65.6 + - - +
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Residues in contact with HIS 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D MET* 4.0 5.8 - - + -
312D VAL* 3.1 23.4 + - + +
314D ARG* 1.3 104.9 + - + +
316D TYR* 1.3 61.3 + - - +
318D MET* 3.2 12.5 + - - +
319D TYR* 2.9 24.4 + - - +
325D THR* 3.5 13.7 - - + +
326D SER 3.9 13.2 + - - -
327D THR* 3.0 29.0 + - - +
501D NDP 3.1 49.8 + + - -
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Residues in contact with TYR 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLU* 3.3 37.5 - - + -
18D MET* 3.3 34.0 - - + +
20D ARG* 2.8 25.7 + - - -
21D ILE* 3.6 26.2 - - + -
312D VAL 3.2 5.3 + - - +
313D THR* 3.0 10.8 + - - +
315D HIS* 1.3 77.0 - - - +
317D ARG* 1.3 68.1 + - - +
319D TYR* 3.2 10.6 + + - +
320D GLN* 2.8 68.2 + - + +
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Residues in contact with ARG 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLU* 3.6 16.7 + - - -
82D ARG* 3.7 5.1 - - - +
85D GLU* 2.9 38.6 + - - -
313D THR* 3.1 25.9 + - + +
314D ARG* 4.0 6.7 - - - +
316D TYR* 1.3 88.9 - - - +
318D MET* 1.3 62.0 + - + +
320D GLN* 3.0 33.5 + - - +
321D LYS* 3.0 47.9 + - - +
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Residues in contact with MET 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D ARG* 3.4 43.9 + - - +
315D HIS* 3.2 13.2 + - - +
317D ARG* 1.3 75.3 - - + +
319D TYR* 1.3 61.5 + - - +
321D LYS* 3.3 6.7 + - - -
323D GLN* 2.8 63.3 + - + +
324D GLU 3.6 19.3 - - - +
325D THR* 4.2 7.6 - - + -
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Residues in contact with TYR 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D MET* 4.0 11.7 - - + -
21D ILE* 3.4 38.2 - - + +
315D HIS 2.9 13.6 + - - +
316D TYR* 3.4 18.4 - + - +
318D MET* 1.3 78.0 - - - +
320D GLN* 1.3 69.3 + - + +
322D GLY* 3.1 13.0 + - - -
323D GLN 4.0 5.6 - - - -
325D THR* 3.7 15.4 - - + +
395D PHE* 3.7 34.2 - + - -
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Residues in contact with GLN 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D TYR* 2.8 55.7 + - + +
317D ARG* 3.0 39.5 + - - +
319D TYR* 1.3 78.8 - - + +
321D LYS* 1.3 62.9 + - + +
322D GLY 3.2 4.2 + - - -
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Residues in contact with LYS 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D ARG* 3.0 41.3 + - - +
318D MET 3.3 1.5 + - - +
320D GLN* 1.3 77.5 + - + +
322D GLY* 1.3 60.8 + - - +
323D GLN* 3.3 33.8 + - - +
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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