Contacts of the helix formed by residues 313 - 329 (chain B) in PDB entry 1MGV
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 ASN 313 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR 3.3 10.3 - - - +
281A MET* 4.0 19.3 - - - +
282A THR* 5.2 3.3 - - + +
76B SER 3.0 16.8 - - - +
77B HIS* 3.2 17.6 + - + +
281B MET* 4.7 1.4 - - - -
283B LEU* 5.1 4.4 - - + +
310B PHE* 3.0 22.4 + - + +
311B MET 3.2 0.6 - - - -
312B GLY* 1.3 74.5 - - - +
314B PRO* 1.3 69.8 - - - +
315B LEU* 3.1 10.9 + - - +
316B ALA* 2.9 40.6 - - + +
317B CYS* 3.0 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLN* 3.7 13.9 - - - +
75B MET* 3.7 20.4 - - + +
76B SER 3.7 4.9 - - - +
77B HIS* 3.6 23.8 - - - +
78B VAL 3.8 15.7 - - - +
85B HIS* 3.4 36.6 - - + +
87B PRO* 3.6 7.6 - - + +
312B GLY 2.8 7.2 - - - +
313B ASN* 1.3 81.9 - - - +
315B LEU* 1.3 57.3 + - - +
317B CYS* 3.2 2.0 + - + +
318B ALA* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 3.3 32.8 - - + -
281A MET* 4.2 7.4 - - + -
315A LEU* 4.1 8.1 - - + -
68B MET* 3.4 42.6 - - + +
71B GLN* 3.9 10.8 - - + -
72B ILE* 3.8 11.9 - - + +
76B SER* 3.1 23.6 + - - +
281B MET* 3.7 23.8 - - + -
313B ASN* 3.2 6.4 - - - +
314B PRO* 1.3 75.0 - - - +
316B ALA* 1.3 64.7 + - - +
318B ALA* 3.2 4.7 + - - +
319B ALA* 3.0 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B THR* 3.8 2.3 - - - +
281B MET* 3.5 22.9 - - + -
282B THR 3.9 19.5 - - - +
283B LEU* 3.8 21.1 - - + +
313B ASN* 2.9 26.2 - - + +
315B LEU* 1.3 75.4 - - - +
317B CYS* 1.3 55.8 + - - +
319B ALA* 3.4 3.0 + - - +
320B ALA* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PRO* 3.6 21.3 - - + +
88B ALA* 4.0 8.3 - - - -
91B LEU* 3.9 21.4 - - + +
108B LEU* 3.9 14.1 - - - -
283B LEU* 4.3 11.7 - - - -
312B GLY* 3.4 30.1 - - - -
313B ASN 3.0 9.1 + - - +
314B PRO* 3.5 7.6 - - + +
316B ALA* 1.3 74.3 - - - +
318B ALA* 1.3 60.9 + - - +
320B ALA* 3.3 2.1 + - - +
321B ASN* 2.9 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 4.0 17.2 - - + +
68B MET* 5.1 0.4 - - - +
71B GLN* 3.6 29.6 - - + +
87B PRO* 4.0 5.1 - - + +
314B PRO 2.8 17.3 + - - +
315B LEU 3.5 7.4 - - - +
317B CYS* 1.3 72.7 - - - +
319B ALA* 1.3 62.0 + - - +
321B ASN* 3.2 10.5 + - - +
322B ALA* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.9 6.3 - - + +
67B ALA* 4.9 1.1 - - - -
68B MET* 3.7 25.0 - - + +
277B THR* 4.1 6.1 - - - +
280B THR* 3.4 26.9 - - + +
281B MET* 4.1 5.2 - - + -
315B LEU 3.0 10.4 + - - +
316B ALA* 3.6 7.6 - - - +
317B CYS 3.3 0.2 - - - -
318B ALA* 1.3 75.7 - - - +
320B ALA* 1.3 58.1 + - - +
322B ALA* 3.2 7.6 + - - +
323B SER* 2.8 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.9 19.5 - - + -
276B LEU* 3.4 26.9 - - + +
277B THR* 3.9 3.7 - - - +
283B LEU* 4.0 14.6 - - + -
316B ALA 3.0 17.4 + - - +
317B CYS 3.6 4.3 - - - +
319B ALA* 1.3 75.6 - - - +
321B ASN* 1.3 57.4 + - - +
323B SER* 3.0 1.4 + - - -
324B LEU* 2.8 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PRO* 3.0 25.8 - - - +
90B GLU* 3.4 33.9 + - - +
91B LEU* 2.9 35.3 - - - +
94B LYS* 3.6 21.8 - - - +
317B CYS 2.9 14.7 + - - +
318B ALA* 3.4 10.7 - - - +
320B ALA* 1.3 75.6 - - - +
322B ALA* 1.3 59.3 + - - +
324B LEU 3.4 0.3 + - - -
325B ALA* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLN* 4.0 10.8 + - + +
64B LEU* 3.8 14.4 - - + -
67B ALA* 3.4 32.3 - - + -
318B ALA 3.0 5.4 + - - +
319B ALA 3.5 7.9 - - - +
321B ASN* 1.3 76.0 - - - +
323B SER* 1.3 64.0 + - - +
325B ALA* 3.3 8.4 + - - +
326B ILE* 3.2 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 4.2 2.8 - - - +
57B HIS* 2.6 40.2 + - - -
64B LEU* 3.5 6.9 - - - +
275B ALA 3.7 7.1 + - - -
276B LEU 3.8 12.5 + - - -
277B THR 3.9 1.1 - - - -
278B GLY* 3.6 18.5 + - - -
319B ALA 2.8 16.5 + - - -
320B ALA 3.5 7.2 - - - -
322B ALA* 1.3 73.1 - - - +
324B LEU* 1.3 62.1 + - - +
326B ILE* 3.2 10.4 + - - +
327B LEU* 3.3 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.5 31.9 - - + -
94B LYS* 3.8 34.1 - - + -
95B LEU* 4.2 8.7 - - + -
98B MET* 3.8 16.7 - - + +
251B PHE* 3.5 37.5 - - + -
275B ALA 6.1 0.2 - - - +
276B LEU* 4.7 9.2 - - + +
320B ALA 2.8 15.9 + - - +
321B ASN 3.8 0.2 - - - +
323B SER* 1.3 76.0 - - - +
325B ALA* 1.3 59.7 + - - +
327B LEU* 3.2 12.3 + - + +
328B GLU* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLN* 5.3 7.6 + - - +
94B LYS* 4.3 4.5 - - - +
321B ASN 2.9 17.7 + - - +
322B ALA* 3.6 10.8 - - - +
324B LEU* 1.3 73.8 - - - +
326B ILE* 1.3 67.8 + - + +
328B GLU* 3.3 29.7 + - - +
329B SER* 3.8 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B HIS* 3.7 40.2 - - + +
61B HIS* 3.6 32.5 - - + +
63B GLN* 3.9 25.8 - - + +
64B LEU* 4.0 7.6 - - + -
322B ALA 3.2 15.2 + - - +
323B SER 3.2 5.5 + - - +
325B ALA* 1.3 77.3 - - - +
327B LEU* 1.3 60.7 + - + +
329B SER* 2.8 33.9 + - - +
331B ASP* 5.2 2.1 + - + +
332B TRP 5.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 4.2 11.7 - - + -
57B HIS* 3.9 17.7 - - + -
98B MET* 5.0 3.1 - - + -
251B PHE* 3.8 43.3 - - + +
257B LEU* 4.5 10.1 - - + -
323B SER* 3.3 11.6 + - - +
324B LEU* 3.2 19.2 + - + +
326B ILE* 1.3 79.4 - - + +
328B GLU* 1.3 62.5 + - - +
330B GLY* 2.9 12.7 + - - -
332B TRP* 3.3 48.9 + - + +
403B TYR* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS* 4.1 30.0 + - + +
98B MET* 6.6 0.2 - - + -
324B LEU* 2.9 18.7 + - + +
325B ALA* 3.5 21.1 - - - +
326B ILE 3.1 0.4 - - - -
327B LEU* 1.3 77.2 - - - +
329B SER* 1.3 62.6 + - - +
330B GLY* 3.0 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ALA 3.8 3.6 + - - -
326B ILE* 2.8 22.6 + - - +
328B GLU* 1.3 77.0 - - - +
330B GLY* 1.3 56.2 + - - +
331B ASP* 3.1 40.9 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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