Contacts of the helix formed by residues 306 - 320 (chain B) in PDB entry 1AX4
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 GLY 306 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A K 4.3 1.2 - - - -
68B GLY* 4.4 2.5 - - - -
69B ASP 3.3 26.2 - - - -
70B GLU* 2.8 16.1 + - - +
77B ASN* 3.6 11.5 - - - +
301B TYR* 5.7 0.4 - - - +
304B LEU 3.8 1.0 + - - -
305B ALA* 1.3 71.5 - - - +
307B ARG* 1.3 62.3 + - - +
309B MET* 3.3 18.2 + - - +
310B ALA* 3.1 18.5 + - - +
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET* 3.8 13.9 - - - +
62A TRP* 4.6 10.4 - - - -
65A MET* 3.8 29.0 - - - +
270A LEU* 6.1 0.4 - - - +
271A ASN* 2.9 41.4 + - - +
272A ILE* 4.2 6.5 - - - +
307A ARG* 4.7 4.8 - - - +
308A ASP* 2.7 30.1 + - - -
65B MET* 3.3 57.6 - - + +
68B GLY* 4.2 5.3 - - - -
70B GLU* 2.9 15.2 + - - +
305B ALA* 3.8 12.1 - - + +
306B GLY* 1.3 77.7 - - - +
308B ASP* 1.3 66.3 + - - +
310B ALA* 3.3 3.3 + - - +
311B ALA 3.0 22.3 + - - -
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Residues in contact with ASP 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 5.0 1.4 - - - +
307A ARG* 2.7 29.8 + - - -
308A ASP* 4.1 11.6 - - - +
65B MET* 4.1 4.3 - - - +
270B LEU* 4.5 4.4 - - + +
272B ILE* 3.6 23.0 - - + +
273B GLY* 5.8 0.2 - - - -
304B LEU* 4.1 21.9 - - + +
305B ALA* 3.0 27.7 + - - +
307B ARG* 1.3 80.4 + - - +
309B MET* 1.3 64.8 + - - +
311B ALA* 3.5 5.9 + - - +
312B MET* 3.0 24.1 + - - +
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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
----------------------------------------------------------
71B ALA 5.8 0.2 - - - +
75B SER* 4.0 24.2 - - - +
77B ASN* 3.9 12.8 - - + +
78B TYR* 4.1 15.0 - - - +
81B LEU* 4.4 12.2 - - + +
96B PRO* 4.2 10.8 - - + -
300B THR 3.3 26.7 - - - +
301B TYR* 3.8 23.1 - - + -
304B LEU* 3.9 25.4 - - + -
305B ALA 3.3 2.9 + - - +
306B GLY* 3.3 20.4 + - - +
308B ASP* 1.3 76.2 - - - +
310B ALA* 1.4 62.9 + - - +
312B MET* 3.3 8.1 + - - +
313B VAL* 3.1 28.1 + - - +
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA* 3.3 39.9 - - + +
68B GLY* 4.2 1.8 - - - -
77B ASN* 3.4 28.4 - - - +
306B GLY 3.1 11.1 + - - +
307B ARG 3.4 8.1 - - - +
309B MET* 1.4 77.4 - - - +
311B ALA* 1.3 62.1 + - - +
313B VAL* 3.3 16.4 + - - +
314B GLN* 3.4 8.8 + - - +
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Residues in contact with ALA 311 (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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307A ARG* 5.8 0.2 - - - +
57B MET* 4.2 13.2 - - - -
61B GLN* 3.6 14.4 + - + +
64B ALA* 4.3 2.6 - - - +
65B MET* 3.9 18.4 - - + -
270B LEU* 3.5 20.3 - - + +
307B ARG 3.0 17.3 + - - +
308B ASP* 3.8 9.6 - - - +
310B ALA* 1.3 76.4 - - - +
312B MET* 1.3 57.1 + - - +
314B GLN* 3.3 3.2 + - - +
315B GLY* 2.8 24.8 + - - -
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Residues in contact with MET 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.8 30.1 - - + -
262B MET* 5.8 0.7 - - - +
264B ALA* 3.8 17.0 - - + -
268B PRO* 5.0 0.7 - - + -
270B LEU* 3.6 20.4 - - + +
273B GLY* 3.9 5.2 - - - -
274B GLY 3.5 39.9 - - - +
275B LEU* 4.6 9.0 - - - -
304B LEU* 3.7 20.0 - - + -
308B ASP 3.0 15.2 + - - +
309B MET* 3.5 7.4 - - - +
310B ALA 3.2 0.2 - - - -
311B ALA* 1.3 72.7 - - - +
313B VAL* 1.3 65.4 + - - +
315B GLY* 4.8 0.2 - - - -
316B LEU* 2.9 35.8 + - + +
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN 4.2 2.0 - - - +
80B ASP* 3.9 25.6 - - + +
81B LEU* 3.7 36.8 - - + +
84B LYS* 3.9 20.6 - - + -
309B MET 3.1 16.2 + - - +
310B ALA* 3.6 10.1 - - - +
311B ALA 3.3 0.2 - - - -
312B MET* 1.3 77.0 - - - +
314B GLN* 1.3 63.7 + - - +
316B LEU* 3.7 14.5 + - - +
317B GLU* 3.7 8.8 + - - +
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Residues in contact with GLN 314 (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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60B HIS* 3.7 22.4 + - - +
61B GLN* 3.5 25.4 - - + +
64B ALA* 4.7 6.3 - - + -
310B ALA 3.4 7.9 + - - +
311B ALA 3.3 7.7 + - - +
312B MET 3.2 0.2 - - - -
313B VAL* 1.3 80.0 - - - +
315B GLY* 1.3 59.8 + - - +
317B GLU* 3.4 12.7 + - - +
318B GLU* 2.8 62.2 + - - +
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Residues in contact with GLY 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLN* 3.4 16.7 - - - +
268B PRO* 3.1 29.0 - - - +
269B LEU* 4.1 0.8 - - - +
311B ALA 2.8 13.6 + - - -
312B MET 3.8 0.9 - - - -
314B GLN* 1.3 75.0 - - - +
316B LEU* 1.3 57.9 + - - +
318B GLU* 3.9 3.8 - - - +
319B GLY* 2.8 30.3 + - - -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.8 27.1 - - + -
84B LYS* 3.9 18.6 - - + -
85B ALA 5.4 2.0 - - - +
88B LEU* 3.9 26.8 - - + +
89B PHE* 4.8 3.1 - - + -
227B PHE* 4.1 16.0 - - + -
228B CYS* 5.1 0.5 - - - -
262B MET* 4.2 13.5 - - + -
268B PRO* 3.9 24.3 + - + +
275B LEU* 5.1 7.9 - - + -
312B MET* 2.9 29.8 + - + +
313B VAL* 3.7 6.1 - - - +
314B GLN 3.3 0.2 - - - -
315B GLY* 1.3 77.4 - - - +
317B GLU* 1.3 57.8 + - - +
319B GLY* 3.9 2.6 + - - -
320B THR* 3.2 24.8 + - - +
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Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LYS* 2.7 39.2 + - - +
247B LYS* 2.7 33.0 + - - +
313B VAL 3.7 4.4 + - - +
314B GLN* 3.4 17.7 + - - +
315B GLY 3.2 0.2 - - - -
316B LEU* 1.3 75.9 - - - +
318B GLU* 1.3 66.2 + - + +
320B THR* 2.8 24.6 + - - -
321B GLU* 3.8 17.7 + - - +
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Residues in contact with GLU 318 (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 SER* 2.5 32.3 + - - -
60B HIS* 4.0 1.7 - - - +
61B GLN* 3.6 6.0 - - - +
269B LEU* 3.8 13.2 - - + +
314B GLN* 2.8 50.1 + - - +
315B GLY* 3.9 1.6 - - - +
317B GLU* 1.3 77.4 - - + +
319B GLY* 1.3 61.4 + - - +
321B GLU* 3.1 37.8 + - - +
324B TYR* 3.8 10.7 - - - -
420B ARG* 3.0 31.9 + - - +
16D LYS* 6.0 2.5 - - - -
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Residues in contact with GLY 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B CYS* 3.3 26.5 - - - +
267B ASP 3.5 24.0 - - - +
268B PRO* 5.0 0.2 - - - -
269B LEU* 3.6 6.9 - - - +
315B GLY 2.8 16.5 + - - -
316B LEU* 3.9 1.8 + - - -
317B GLU 3.3 0.6 - - - -
318B GLU* 1.3 73.3 - - - +
320B THR* 1.3 57.1 + - - +
321B GLU 3.4 0.4 - - - -
324B TYR* 4.1 5.8 - - - -
325B LEU* 3.6 14.9 - - - +
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Residues in contact with THR 320 (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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88B LEU* 4.2 18.2 - - + -
227B PHE* 5.0 0.7 - - + -
228B CYS* 4.0 10.1 - - - -
246B ILE* 3.4 29.7 - - - +
247B LYS* 3.6 21.8 - - + +
250B ILE* 3.7 23.3 - - + -
316B LEU 3.2 19.5 - - - +
317B GLU* 2.8 16.3 + - - -
318B GLU 3.2 0.2 - - - -
319B GLY* 1.3 74.4 - - - +
321B GLU* 1.3 65.7 + - - +
322B GLU 3.3 3.1 + - - -
325B LEU* 4.0 1.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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