Contacts of the helix formed by residues 300 - 310 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 4.1 21.1 - - + +
50B LEU* 4.4 11.4 - - + -
51B GLY* 3.3 31.2 - - - +
54B ILE* 4.3 7.7 - - + +
55B ASN* 4.4 2.0 - - - +
87B VAL* 5.7 0.2 - - + -
297B THR* 3.0 16.8 + - - +
298B SER 3.1 1.6 + - - -
299B ALA* 1.3 90.0 - - + +
301B TYR* 1.3 64.9 + - - +
302B ASN 3.3 2.5 - - - -
303B PRO* 3.1 21.7 - - - +
304B VAL* 3.4 15.3 - - + +
1407B 4E6 4.1 30.3 - - + -
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Residues in contact with TYR 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ALA* 5.3 2.9 - - - +
257B MET 4.1 3.0 + - - -
260B ALA* 3.4 27.8 - - + -
261B PHE* 3.1 39.8 - - - +
264B CYS* 3.9 17.2 - - + +
265B TRP* 4.9 0.9 + - - -
297B THR* 3.2 24.2 + - - +
298B SER* 3.4 28.5 + - - -
300B VAL* 1.3 80.2 - - - +
302B ASN* 1.3 95.2 + - - +
304B VAL* 3.2 11.3 + - - +
305B ILE* 3.1 29.6 + - + +
1407B 4E6 3.8 27.5 - - + +
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Residues in contact with ASN 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 4.3 6.1 - - + +
79B LEU* 3.6 36.6 - - + +
83B ASP* 4.7 5.8 - - - +
124B ALA* 4.8 8.8 - - - +
128B LEU* 6.1 0.2 - - - +
257B MET* 3.2 33.6 + - + +
298B SER 4.5 8.2 + - - +
300B VAL 3.3 0.2 - - - -
301B TYR* 1.3 106.3 + - - +
303B PRO* 1.3 71.5 - - + +
304B VAL 3.1 0.5 + - - -
305B ILE* 3.1 6.6 + - - +
306B TYR* 3.0 22.3 + - - +
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Residues in contact with PRO 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 3.8 21.1 - - + +
55B ASN* 3.4 25.8 - - - +
58B THR* 3.4 29.4 - - + +
76B LEU* 5.3 0.9 - - + +
79B LEU* 6.3 0.2 - - + -
80B ALA* 5.5 1.6 - - - +
83B ASP* 4.1 7.6 - - - +
300B VAL 3.1 16.6 - - - +
302B ASN* 1.3 95.9 - - + +
304B VAL* 1.3 55.0 + - - +
306B TYR* 3.3 9.7 - - + +
307B ILE* 3.0 37.8 + - + +
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Residues in contact with VAL 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 5.4 3.8 - - + -
46A LEU* 4.5 20.2 - - + -
50B LEU* 6.1 0.7 - - + -
54B ILE* 3.7 19.3 - - + -
300B VAL* 3.4 18.2 - - + +
301B TYR* 3.5 11.2 - - - +
302B ASN 3.1 0.8 - - - -
303B PRO* 1.3 74.8 - - - +
305B ILE* 1.3 67.8 + - - +
307B ILE* 3.5 4.4 + - - +
308B MET* 3.1 48.7 + - + +
1407B 4E6 3.9 32.8 - - + -
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Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B MET* 3.8 15.7 - - + -
256B ILE* 4.0 18.2 - - + -
257B MET* 3.7 33.4 - - + -
260B ALA* 4.0 6.1 - - + -
301B TYR* 3.1 32.4 + - + +
302B ASN* 3.1 7.3 + - - +
304B VAL* 1.3 76.2 - - - +
306B TYR* 1.3 53.1 + - - +
308B MET* 2.9 6.3 + - - -
309B MET* 2.6 67.1 + - - +
1407B 4E6 4.5 13.0 - - + -
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Residues in contact with TYR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B THR* 4.0 13.0 - - + -
62B THR* 4.7 4.0 + - - -
68B LEU* 5.1 0.5 - - - +
72B LEU* 4.5 9.6 - - + -
73B ASN* 3.1 34.8 + - - +
76B LEU* 3.1 40.6 - - + -
253B MET* 3.3 27.7 - - + +
302B ASN 3.0 4.1 + - - +
303B PRO* 3.3 11.7 - - + +
305B ILE* 1.3 77.4 - - - +
307B ILE* 1.3 57.6 + - - +
308B MET 3.1 0.2 + - - -
310B ASN* 2.8 48.7 + - + +
313B PHE* 3.4 57.7 - + + +
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 4.3 19.7 - - + -
54B ILE* 4.6 13.9 - - + -
57B LEU* 5.0 3.1 - - + -
58B THR* 5.3 1.3 - - - +
303B PRO* 3.0 22.3 + - + +
304B VAL* 4.0 4.5 - - - +
306B TYR* 1.3 74.8 - - - +
308B MET* 1.3 58.8 + - + +
310B ASN 4.4 0.2 - - - -
313B PHE* 3.8 24.9 - - + -
314B ARG* 3.0 37.1 + - + +
317B MET* 3.4 41.3 - - + -
1401B HTO 3.7 19.6 + - + -
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Residues in contact with MET 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A SER* 4.5 8.7 - - - +
39A MET* 4.4 18.6 - - + -
42A ALA* 3.6 31.0 - - + -
304B VAL* 3.1 35.0 - - + +
305B ILE* 2.9 6.1 + - - +
307B ILE* 1.3 82.8 - - + +
309B MET* 1.3 64.6 + - + +
310B ASN 3.6 0.4 - - - -
314B ARG* 3.4 6.4 + - - -
1401B HTO 3.3 48.0 + - + +
1407B 4E6 5.3 7.6 - - + -
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Residues in contact with MET 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B GLU* 3.9 18.7 - - - +
250B VAL* 5.9 0.2 - - - -
252B ARG* 3.8 24.7 - - + +
253B MET* 3.8 24.9 - - + +
256B ILE* 3.6 34.1 - - + -
305B ILE* 2.6 40.7 + - + +
306B TYR 3.6 0.4 - - - -
308B MET* 1.3 80.6 - - + +
310B ASN* 1.3 61.5 + - - +
311B LYS 4.1 1.6 - - - -
314B ARG* 4.4 1.6 - - - +
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Residues in contact with ASN 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 5.5 0.2 - - - +
72B LEU* 3.8 22.0 - - - +
73B ASN* 4.9 4.1 + - - +
249B GLU* 3.7 14.6 + - - -
250B VAL* 4.7 8.1 - - - +
253B MET* 4.2 2.8 - - - -
306B TYR* 2.8 33.4 + - + +
308B MET 3.6 2.0 - - - +
309B MET* 1.3 80.6 + - - +
311B LYS* 1.3 56.4 + - - +
312B GLN* 3.8 12.0 + - - +
313B PHE* 2.9 33.0 + - + +
314B ARG* 2.8 38.8 + - - +
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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