Contacts of the helix formed by residues 304 - 313 (chain A) in PDB entry 3ORY
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 ASP 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ASP 5.5 1.1 - - - +
145A ALA* 2.7 19.2 + - - +
302A THR 3.5 2.9 + - - +
303A PRO* 1.3 72.7 - - - +
305A PRO* 1.4 65.2 - - - +
306A ASP* 3.5 9.0 + - - +
307A ALA* 3.3 29.5 + - + +
308A VAL* 3.1 23.2 + - - +
310A ARG* 5.2 2.8 + - - -
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Residues in contact with PRO 305 (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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303A PRO 3.3 12.5 - - - +
304A ASP* 1.4 85.6 - - - +
306A ASP* 1.3 58.9 + - - +
308A VAL* 3.2 4.0 + - + +
309A LYS* 2.9 28.4 + - - +
327A LEU* 3.7 30.6 - - + +
331A VAL* 4.1 23.8 - - + -
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Residues in contact with ASP 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ASP* 3.3 7.6 + - - +
305A PRO* 1.3 78.7 - - - +
307A ALA* 1.3 57.5 + - - +
309A LYS* 3.2 24.7 + - - +
310A ARG* 2.8 60.4 + - - +
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Residues in contact with ALA 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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145A ALA* 3.7 17.0 - - + -
304A ASP* 3.1 32.2 + - + +
306A ASP* 1.3 73.9 - - - +
308A VAL* 1.3 65.4 + - - +
310A ARG* 3.4 28.6 + - - +
311A ILE* 3.1 29.6 + - + +
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Residues in contact with VAL 308 (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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66A PHE* 3.6 30.7 - - + -
142A LEU* 4.1 7.9 - - + -
145A ALA* 3.6 28.9 - - + +
146A MET* 4.0 14.4 - - + -
303A PRO* 6.0 0.4 - - + -
304A ASP 3.1 15.6 + - - +
305A PRO 3.2 6.9 + - - +
307A ALA* 1.3 76.6 - - - +
309A LYS* 1.3 62.1 + - - +
311A ILE* 3.3 2.9 + - - +
312A LEU* 2.9 37.2 + - + +
323A VAL* 4.5 1.3 - - + -
327A LEU* 3.9 21.3 - - + -
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Residues in contact with LYS 309 (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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305A PRO 2.9 14.2 + - - +
306A ASP* 3.4 28.6 + - - +
308A VAL* 1.3 76.5 - - - +
310A ARG* 1.3 71.1 + - - +
313A VAL* 2.8 40.7 + - + -
314A ASP* 2.8 37.1 + - - +
320A ILE* 3.8 29.6 - - + -
323A VAL* 4.6 7.2 - - + -
327A LEU* 4.6 3.5 - - + +
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Residues in contact with ARG 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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304A ASP* 5.2 2.4 + - - -
306A ASP* 2.8 49.5 + - - +
307A ALA* 3.7 35.3 + - - +
308A VAL 3.3 0.2 - - - -
309A LYS* 1.3 78.6 - - - +
311A ILE* 1.3 59.0 + - + +
314A ASP* 3.3 23.8 - - + +
315A GLU* 2.9 40.1 + - - +
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Residues in contact with ILE 311 (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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62A LEU* 4.9 5.2 - - + -
138A ASP* 5.0 7.6 - - + +
141A SER* 3.7 39.5 - - - +
142A LEU* 3.9 18.2 - - + -
145A ALA* 4.1 9.6 - - + -
307A ALA* 3.1 19.1 + - + +
308A VAL* 3.8 3.1 - - - +
310A ARG* 1.3 78.3 - - + +
312A LEU* 1.3 72.9 + - + +
315A GLU* 3.3 18.3 - - - +
316A HIS* 3.1 41.6 + - + +
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Residues in contact with LEU 312 (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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62A LEU* 4.2 19.3 - - + +
66A PHE* 3.5 46.0 - - + -
142A LEU* 4.1 20.0 - - + -
308A VAL* 2.9 30.1 + - + +
311A ILE* 1.3 75.7 - - + +
313A VAL* 1.3 61.1 + - + +
316A HIS* 3.1 7.0 + - - -
317A ASP 3.0 10.9 + - - -
318A PHE* 3.0 57.0 + - + -
323A VAL* 4.1 11.9 - - + -
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Residues in contact with VAL 313 (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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309A LYS* 2.8 35.1 + - + +
312A LEU* 1.3 70.5 - - - +
314A ASP* 1.3 69.8 + - - +
317A ASP* 2.9 28.2 + - - +
318A PHE 3.5 22.0 - - - +
320A ILE* 3.9 33.2 - - + +
323A VAL* 3.9 26.7 - - + -
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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