Contacts of the helix formed by residues 306 - 310 (chain A) in PDB entry 1HDZ
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 MET 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A ASN* 2.8 28.6 + - - +
305A PRO* 1.4 71.5 - - - +
307A LEU* 1.4 61.4 + - + +
308A LEU 2.9 1.8 + - - -
309A LEU* 3.1 43.4 + - + +
310A THR* 3.6 27.2 + - + +
57B LEU* 6.1 2.5 - - - -
110B TYR* 5.4 0.7 - - - +
116B LEU* 5.3 17.5 - - + +
117B GLY* 5.9 7.0 - - - +
294B VAL* 5.2 5.4 - - - -
295B PRO* 3.9 22.2 - - + +
296B PRO 6.0 0.2 - - - +
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Residues in contact with LEU 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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276A MET* 4.1 19.5 - - + -
279A LEU* 4.1 15.9 - - + -
280A LEU* 3.8 29.4 - - + -
303A ILE* 4.5 4.5 - - + -
304A ASN* 2.9 35.1 + - + +
306A MET* 1.4 77.7 - - + +
308A LEU* 1.3 59.7 + - - +
310A THR* 3.6 5.1 + - - -
312A ARG* 2.9 47.8 + - - +
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 4.9 4.9 - - + -
303A ILE* 3.7 22.0 - - + -
305A PRO 2.9 8.4 + - - +
307A LEU* 1.3 81.7 - - + +
309A LEU* 1.3 61.2 + - - +
310A THR 3.3 2.7 - - - -
311A GLY 3.2 9.0 + - - -
312A ARG* 3.4 33.8 + - + +
314A TRP* 4.1 17.0 - - + -
291B ILE* 4.1 12.6 - - + -
314B TRP* 3.5 58.3 - - + +
316B GLY* 3.0 27.0 + - - +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PRO 3.2 9.7 + - - +
306A MET* 3.1 29.7 + - + +
308A LEU* 1.3 73.9 - - - +
310A THR* 1.3 57.4 + - - +
311A GLY 3.0 3.1 + - - -
116B LEU* 5.4 4.3 - - + -
291B ILE* 4.0 17.9 - - + +
292B VAL 3.7 2.9 - - - +
293B GLY 3.4 18.2 - - - +
294B VAL* 3.8 20.2 - - + -
295B PRO* 3.8 22.0 - - + -
316B GLY* 3.8 4.9 - - - -
317B ALA* 2.9 38.0 + - - +
318B VAL* 3.5 12.9 + - + +
377B NAD 3.7 21.3 - - - +
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Residues in contact with THR 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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284A GLU* 2.8 42.4 + - + +
285A ALA* 3.5 4.5 - - - +
306A MET* 3.6 31.7 + - + +
307A LEU* 3.6 8.7 + - - -
309A LEU* 1.3 71.2 - - - +
311A GLY* 1.3 54.5 + - - +
109B ASN* 5.2 1.4 - - - +
110B TYR* 3.4 59.0 - - + +
117B GLY* 5.7 0.4 - - - -
317B ALA* 4.9 0.9 - - - -
318B VAL* 4.2 11.2 + - + +
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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