Contacts of the helix formed by residues 306 - 320 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A GLY* 4.4 2.0 - - - -
69A ASP 3.3 25.1 - - - -
70A GLU* 2.8 16.5 + - - +
77A ASN* 3.7 10.2 - - - +
301A TYR* 5.6 0.8 - - - +
304A LEU 3.7 1.2 + - - -
305A ALA* 1.3 70.2 - - - +
307A ARG* 1.3 59.9 + - - +
309A MET* 3.1 18.4 + - - +
310A ALA* 3.0 22.0 + - - +
500B K 4.3 1.4 - - - -
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Residues in contact with ARG 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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65A MET* 3.3 59.4 - - + +
68A GLY* 4.2 7.1 - - - -
70A GLU* 3.0 17.3 + - - +
305A ALA* 3.7 11.2 - - + +
306A GLY* 1.3 75.3 - - - +
308A ASP* 1.4 67.6 + - - +
310A ALA* 3.3 3.0 + - - +
311A ALA 3.1 21.7 + - - -
57B MET* 3.7 14.1 - - - +
62B TRP* 4.6 10.7 - - - -
65B MET* 3.8 28.8 - - - +
271B ASN* 3.1 35.6 + - - +
272B ILE* 4.3 10.5 - - - +
307B ARG* 4.7 4.8 - - - +
308B ASP* 2.7 29.3 + - - -
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Residues in contact with ASP 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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65A MET* 4.0 4.9 - - - +
270A LEU* 4.5 4.2 - - + +
272A ILE* 3.6 28.9 - - + +
304A LEU* 4.2 17.5 - - + +
305A ALA* 3.0 26.6 + - - +
307A ARG* 1.4 82.1 + - - +
309A MET* 1.3 65.4 + - - +
311A ALA* 3.5 5.0 + - - +
312A MET* 3.0 23.0 + - - +
272B ILE* 5.1 1.2 - - - +
307B ARG* 2.7 30.0 + - - -
308B ASP* 4.1 11.3 - - - +
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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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75A SER* 3.9 25.1 - - - +
77A ASN* 3.8 13.2 - - + +
78A TYR* 4.0 16.6 - - - +
81A LEU* 4.3 13.3 - - + +
96A PRO* 4.2 12.3 - - + -
300A THR 3.3 26.9 - - - +
301A TYR* 3.8 21.8 - - + -
304A LEU* 4.1 24.2 - - + -
305A ALA 3.3 3.3 + - - +
306A GLY* 3.1 18.4 + - - +
308A ASP* 1.3 77.1 - - - +
310A ALA* 1.3 62.4 + - - +
312A MET* 3.2 7.9 + - - +
313A VAL* 3.1 26.7 + - - +
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Residues in contact with ALA 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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64A ALA* 3.4 39.6 - - + +
68A GLY* 4.2 2.2 - - - -
77A ASN* 3.4 30.0 - - - +
306A GLY 3.0 10.6 + - - +
307A ARG 3.5 7.6 - - - +
308A ASP 3.2 0.4 - - - -
309A MET* 1.3 77.1 - - - +
311A ALA* 1.3 61.0 + - - +
313A VAL* 3.3 17.2 + - - +
314A GLN* 3.4 8.1 + - - +
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Residues in contact with ALA 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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57A MET* 4.2 13.7 - - - -
61A GLN* 3.6 13.6 + - + +
64A ALA* 4.4 2.2 - - - +
65A MET* 3.8 20.2 - - + -
270A LEU* 3.5 18.6 - - + +
307A ARG 3.1 15.9 + - - +
308A ASP* 3.9 7.9 - - - +
310A ALA* 1.3 75.5 - - - +
312A MET* 1.4 52.5 + - - +
314A GLN* 3.3 3.6 + - - +
315A GLY* 2.7 34.0 + - - -
307B ARG* 5.7 0.2 - - - +
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Residues in contact with MET 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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81A LEU* 3.8 27.8 - - + -
262A MET* 5.8 1.1 - - - +
264A ALA* 3.8 17.9 - - + -
268A PRO* 5.0 1.1 - - + -
270A LEU* 3.5 23.7 - - + +
273A GLY* 4.0 1.3 - - - -
274A GLY 3.5 37.9 - - - +
275A LEU* 4.6 9.9 - - - -
304A LEU* 3.7 19.3 - - + -
308A ASP 3.0 12.9 + - - +
309A MET* 3.5 9.6 - - - +
310A ALA 3.2 0.2 - - - -
311A ALA* 1.4 74.4 - - - +
313A VAL* 1.3 66.1 + - - +
315A GLY* 4.8 0.4 - - - -
316A LEU* 2.9 39.7 + - + +
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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
----------------------------------------------------------
77A ASN* 4.2 2.0 - - + +
80A ASP* 3.9 24.7 - - + +
81A LEU* 3.6 37.2 - - + +
84A LYS* 4.0 20.1 - - + +
309A MET 3.1 15.3 + - - +
310A ALA* 3.3 10.5 + - - +
312A MET* 1.3 78.4 - - - +
314A GLN* 1.3 60.9 + - - +
316A LEU* 3.7 9.7 + - - +
317A GLU* 3.7 12.6 + - - +
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Residues in contact with GLN 314 (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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60A HIS* 3.7 23.3 + - + +
61A GLN* 3.5 26.5 - - + +
64A ALA* 4.8 4.7 - - + +
310A ALA 3.4 7.4 + - - +
311A ALA 3.3 7.1 + - - +
312A MET 3.2 0.4 - - - -
313A VAL* 1.3 77.6 - - - +
315A GLY* 1.3 60.7 + - - +
317A GLU* 3.2 13.8 + - - +
318A GLU* 2.9 64.1 + - - +
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Residues in contact with GLY 315 (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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61A GLN* 3.3 17.6 - - - +
268A PRO* 3.0 30.7 - - - +
269A LEU* 4.7 0.4 - - - -
311A ALA 2.7 17.2 + - - -
312A MET 3.8 0.9 - - - -
314A GLN* 1.3 70.5 - - - +
316A LEU* 1.3 57.9 + - - +
318A GLU* 4.0 3.7 - - - +
319A GLY* 2.9 29.5 + - - -
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Residues in contact with LEU 316 (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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81A LEU* 3.9 25.8 - - + -
84A LYS* 4.0 19.1 - - + -
85A ALA 5.5 2.0 - - - +
88A LEU* 3.9 20.4 - - + +
89A PHE* 4.8 3.1 - - + -
227A PHE* 4.0 23.0 - - + -
262A MET* 4.2 13.2 - - + -
268A PRO* 3.9 24.8 - - + +
275A LEU* 5.1 7.6 - - + -
312A MET* 2.9 30.2 + - + +
313A VAL 3.8 4.7 - - - +
315A GLY* 1.3 75.9 - - - +
317A GLU* 1.3 62.1 + - - +
319A GLY* 3.9 1.3 + - - -
320A THR* 3.2 24.8 + - - +
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Residues in contact with GLU 317 (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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84A LYS* 2.8 27.5 + - - +
88A LEU* 6.0 0.2 - - - -
247A LYS* 2.7 37.2 + - - -
313A VAL 3.7 4.9 + - - +
314A GLN* 3.2 19.7 + - - +
316A LEU* 1.3 76.8 - - - +
318A GLU* 1.3 63.8 + - - +
320A THR* 2.6 28.7 + - - -
321A GLU* 3.8 17.7 + - - +
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Residues in contact with GLU 318 (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 SER* 2.5 32.3 + - - -
60A HIS* 4.0 2.1 - - - +
61A GLN* 3.5 5.9 - - - +
269A LEU* 3.7 13.6 - - + +
314A GLN* 2.9 46.5 + - - +
315A GLY 3.4 1.3 + - - +
317A GLU* 1.3 75.0 - - + +
319A GLY* 1.3 61.4 + - - +
321A GLU* 3.2 39.2 + - - +
324A TYR* 3.9 10.6 - - - +
420A ARG* 2.9 37.3 + - - +
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Residues in contact with GLY 319 (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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228A CYS* 3.2 28.3 - - - +
267A ASP 3.7 19.5 - - - -
268A PRO* 5.2 0.4 - - - -
269A LEU* 3.7 7.6 - - - +
315A GLY 2.9 17.2 + - - -
316A LEU 4.4 1.3 - - - -
317A GLU 3.3 0.2 - - - -
318A GLU* 1.3 74.8 - - - +
320A THR* 1.3 58.6 + - - +
321A GLU 3.4 0.2 - - - -
324A TYR* 4.2 6.5 - - - -
325A LEU* 3.6 14.2 - - - +
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Residues in contact with THR 320 (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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88A LEU* 4.3 17.5 - - + -
227A PHE* 5.0 0.7 - - + -
228A CYS* 4.0 9.4 - - - -
246A ILE* 3.3 31.5 - - - +
247A LYS* 3.6 23.7 - - + +
250A ILE* 3.8 23.1 - - + -
316A LEU 3.2 18.8 - - - +
317A GLU* 2.6 18.4 + - - -
319A GLY* 1.3 79.8 - - - +
321A GLU* 1.3 62.9 + - - +
322A GLU 3.3 0.9 + - - -
325A LEU* 4.0 2.9 - - - -
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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