Contacts of the helix formed by residues 300 - 310 (chain A) in PDB entry 3OAX
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 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LEU* 4.2 18.4 - - + +
50A LEU* 4.5 5.4 - - + -
51A GLY* 3.6 31.6 - - - +
54A ILE* 4.4 11.5 - - + +
55A ASN* 4.4 2.0 - - - +
91A PHE* 5.8 0.2 - - + -
297A THR 2.9 9.2 + - - +
299A ALA* 1.3 89.8 - - + +
301A TYR* 1.3 64.7 + - - +
302A ASN 3.4 2.7 - - - -
303A PRO* 3.3 14.2 - - - +
304A VAL* 3.1 21.2 + - + +
1410A 4E6 3.6 35.2 - - + -
46B LEU* 4.6 6.3 - - + -
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Residues in contact with TYR 301 (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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124A ALA* 5.1 2.4 - - - +
257A MET 4.3 1.8 - - - -
260A ALA* 3.5 28.7 - - + -
261A PHE* 3.1 40.2 + - - +
264A CYS* 4.1 17.3 - - + -
265A TRP* 4.7 0.9 + - - -
297A THR* 3.2 12.7 + - - +
298A SER* 3.4 41.4 + - - -
300A VAL* 1.3 76.7 - - - +
302A ASN* 1.3 98.1 + - - +
304A VAL* 3.0 13.3 + - - +
305A ILE* 3.1 20.1 + - + +
1410A 4E6 3.7 34.7 - - + +
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Residues in contact with ASN 302 (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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76A LEU* 4.3 14.8 - - + +
79A LEU* 4.2 18.3 - - + +
83A ASP* 4.6 6.8 - - - +
124A ALA* 4.4 11.7 - - - +
128A LEU* 5.9 0.6 - - - +
257A MET* 3.6 33.7 + - - +
298A SER 4.0 10.2 + - - +
300A VAL 3.4 0.2 - - - -
301A TYR* 1.3 112.6 + - - +
303A PRO* 1.3 73.1 - - + +
305A ILE* 2.9 17.8 + - - +
306A TYR* 3.0 11.6 + - - +
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Residues in contact with PRO 303 (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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54A ILE* 3.6 16.6 - - + -
55A ASN* 3.2 26.9 - - - +
58A THR* 3.5 28.3 - - + +
76A LEU* 4.7 5.6 - - + +
79A LEU* 6.0 0.7 - - + -
80A ALA* 5.1 3.1 - - + +
83A ASP* 3.8 8.5 - - - +
300A VAL 3.3 14.4 - - - +
302A ASN* 1.3 95.0 - - + +
304A VAL* 1.3 55.9 + - - +
306A TYR* 3.4 9.1 - - + +
307A ILE* 2.9 38.4 + - + +
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Residues in contact with VAL 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 4.7 4.3 - - + -
300A VAL* 3.1 22.4 - - + +
301A TYR* 3.0 9.1 + - - +
303A PRO* 1.3 76.9 - - - +
305A ILE* 1.3 55.2 + - - +
307A ILE* 4.1 0.6 - - - -
308A MET* 2.8 41.4 + - + +
1410A 4E6 4.1 16.6 - - + -
1508A HTG 4.4 0.7 - - + -
42B ALA* 4.0 29.4 - - + +
45B PHE* 3.9 31.2 - - + -
46B LEU* 4.1 22.0 - - + -
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Residues in contact with ILE 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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253A MET* 3.8 14.4 - - + -
256A ILE* 4.0 17.7 - - + -
257A MET* 4.1 19.5 - - + -
260A ALA* 3.8 17.7 - - + -
301A TYR* 3.1 34.5 + - + +
302A ASN* 2.9 7.2 + - - +
304A VAL* 1.3 74.2 - - - +
306A TYR* 1.3 56.4 + - - +
309A MET* 2.7 65.6 + - - +
1410A 4E6 4.3 8.3 - - + -
1508A HTG 4.0 19.5 - - + -
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Residues in contact with TYR 306 (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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58A THR* 4.1 11.2 - - + -
62A THR* 4.7 2.9 + - - -
72A LEU* 4.4 3.6 - - + -
73A ASN* 2.6 37.1 + - - +
76A LEU* 3.5 58.1 - - + -
253A MET* 3.6 19.0 - - + -
302A ASN 3.0 5.8 + - - +
303A PRO 3.4 9.4 - - - +
305A ILE* 1.3 77.4 - - - +
307A ILE* 1.3 57.2 + - - +
310A ASN* 2.9 48.2 + - + +
313A PHE* 3.4 59.8 - + + -
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Residues in contact with ILE 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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54A ILE* 5.1 2.5 - - + +
57A LEU* 6.1 1.6 - - + -
58A THR* 4.4 13.0 - - - +
303A PRO* 2.9 20.7 + - + +
304A VAL* 4.1 3.4 - - - +
306A TYR* 1.3 74.8 - - - +
308A MET* 1.3 64.1 + - - +
309A MET 3.7 0.2 + - - -
310A ASN 4.2 0.9 + - - -
313A PHE* 3.9 24.9 - - + -
314A ARG* 3.0 41.1 + - + +
317A MET* 3.6 37.7 - - + -
45B PHE* 3.4 36.8 - - + -
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Residues in contact with MET 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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304A VAL* 2.8 32.1 + - + +
305A ILE 4.0 1.8 - - - +
307A ILE* 1.3 86.7 - - - +
309A MET* 1.3 60.6 + - - +
314A ARG* 3.1 15.1 + - - +
1508A HTG 4.0 36.6 - - + -
38B SER* 4.1 10.0 + - - +
41B ALA* 2.9 50.3 - - + +
42B ALA* 3.7 5.2 - - - +
45B PHE* 4.3 15.5 - - - -
95B LEU* 4.5 3.8 - - + -
99B LEU* 3.1 27.2 - - + +
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Residues in contact with MET 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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249A GLU* 3.3 27.3 - - - +
252A ARG* 4.0 9.4 - - + -
253A MET* 3.8 37.6 - - + +
256A ILE* 3.8 15.0 - - + -
305A ILE* 2.7 40.6 + - - +
306A TYR 3.6 0.7 - - - -
308A MET* 1.3 79.0 - - - +
310A ASN* 1.3 58.5 + - - +
311A LYS 4.0 0.2 - - - -
314A ARG* 5.0 0.4 - - - -
1508A HTG 3.4 76.7 + - + +
38B SER* 5.3 0.7 - - - +
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Residues in contact with ASN 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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68A LEU* 5.9 0.2 - - - +
72A LEU* 3.8 25.9 - - - +
73A ASN* 5.3 3.7 + - - +
249A GLU* 3.5 15.3 + - - -
250A VAL* 4.6 5.5 - - - +
253A MET* 4.4 3.2 - - - -
306A TYR* 2.9 29.8 + - + +
307A ILE 4.2 0.4 + - - -
308A MET 3.7 1.6 - - - -
309A MET* 1.3 78.5 + - - +
311A LYS* 1.3 66.7 + - - +
312A GLN* 3.4 12.8 + - - +
313A PHE* 2.7 36.0 + - + +
314A ARG* 3.0 24.5 + - - +
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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