Contacts of the helix formed by residues 305 - 320 (chain F) in PDB entry 5MGX
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 305 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709A ASP* 5.8 0.6 + - - -
272F VAL* 4.5 2.4 - - - +
276F ASN* 2.9 31.3 + - - +
298F VAL* 3.8 10.1 - - + +
299F LEU* 3.9 0.4 - - - +
302F GLN* 3.1 44.8 + - + +
303F PRO 3.5 1.4 - - - -
304F ASP* 1.3 73.1 - - - +
306F ILE* 1.3 58.9 + - - +
307F LYS* 3.3 8.3 + - - +
308F ALA* 3.0 24.0 + - + +
309F LEU* 3.0 30.8 + - - +
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Residues in contact with ILE 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A THR* 4.0 27.8 - - + +
705A MET* 3.9 11.0 - - + -
304F ASP 3.3 6.3 + - - +
305F ASN* 1.3 72.0 + - - +
307F LYS* 1.4 60.1 + - + +
309F LEU* 3.4 8.7 + - - +
310F PHE* 2.9 29.9 + - - +
332F ALA* 3.4 33.6 - - + +
335F LEU* 4.3 11.2 - - + -
336F GLU* 3.6 38.6 - - + +
342F ILE* 3.7 10.1 - - + -
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Residues in contact with LYS 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A THR* 3.8 23.3 - - + -
704A GLU 3.4 22.0 + - - -
705A MET* 4.2 13.0 - - - -
707A GLU* 3.1 31.9 + - - +
708A VAL 4.6 0.2 - - - -
709A ASP* 3.1 36.3 + - - +
276F ASN* 3.8 9.6 - - - +
305F ASN* 3.3 9.7 + - - +
306F ILE* 1.4 79.3 - - + +
308F ALA* 1.3 56.2 + - - +
310F PHE* 3.4 1.6 + - - +
311F ARG* 2.9 58.5 + - - +
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Residues in contact with ALA 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276F ASN* 3.6 11.1 + - - +
295F CYS* 3.7 10.7 - - - +
298F VAL* 3.6 33.7 - - + -
299F LEU* 3.8 22.2 - - + +
305F ASN* 3.0 11.4 + - - +
307F LYS* 1.3 72.4 - - - +
309F LEU* 1.3 60.4 + - - +
311F ARG* 4.5 3.6 - - - -
312F LYS* 3.0 30.5 + - - +
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Residues in contact with LEU 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F LEU* 3.7 25.1 - - + -
303F PRO 3.8 18.2 - - - +
304F ASP* 4.3 0.7 - - - -
305F ASN 3.0 23.2 + - - +
306F ILE* 3.7 4.0 - - - +
308F ALA* 1.3 72.7 - - - +
310F PHE* 1.3 59.0 + - - +
312F LYS 3.3 1.4 + - - -
313F GLY* 2.9 25.6 + - - -
328F ILE* 3.2 35.7 - - + +
331F ALA* 4.5 11.4 - - + +
332F ALA* 3.9 21.1 - - + +
335F LEU* 3.9 26.5 - - + -
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Residues in contact with PHE 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A MET* 3.7 38.1 - - + -
706A GLU* 4.8 3.1 - - - -
283F LEU* 6.0 0.2 - - + -
306F ILE 2.9 17.4 + - - +
307F LYS 3.8 2.5 - - - +
309F LEU* 1.3 75.6 - - - +
311F ARG* 1.3 67.5 + - + +
313F GLY* 3.4 1.4 + - - -
314F LYS* 2.9 54.6 + - + +
329F LEU* 3.9 16.4 - - + +
332F ALA* 4.3 7.7 - - + +
341F THR* 3.7 28.7 - - + -
342F ILE* 4.0 17.3 - - + -
345F GLU* 3.6 39.5 - - + -
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Residues in contact with ARG 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A MET* 5.6 1.6 - - - +
706A GLU* 3.9 20.2 - - - +
707A GLU 2.8 28.7 + - - -
708A VAL* 4.9 0.4 - - - +
709A ASP* 5.6 0.8 + - - -
276F ASN* 3.1 45.2 + - - +
277F ASN* 4.5 3.0 + - - +
279F ALA* 4.7 2.9 - - + -
280F ALA* 3.6 32.5 - - - +
283F LEU* 4.0 20.6 - - + +
295F CYS* 3.7 17.3 - - - -
307F LYS* 2.9 38.8 + - - +
310F PHE* 1.3 81.3 - - + +
312F LYS* 1.4 60.9 + - - +
314F LYS* 3.9 5.8 - - - +
315F VAL* 3.0 34.9 + - + +
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Residues in contact with LYS 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F LEU* 3.8 18.4 - - + -
295F CYS* 3.6 15.1 - - + -
296F SER* 3.1 28.3 + - - +
299F LEU* 3.9 20.3 - - + +
308F ALA 3.0 19.6 + - - +
309F LEU 3.3 3.3 + - - +
311F ARG* 1.4 74.6 - - - +
313F GLY* 1.3 57.5 + - - +
315F VAL* 3.4 5.3 + - - +
316F LEU* 2.9 55.0 + - + +
328F ILE* 4.1 20.0 - - + +
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Residues in contact with GLY 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309F LEU 2.9 13.6 + - - -
310F PHE 3.7 3.4 - - - -
312F LYS* 1.3 75.7 - - - +
314F LYS* 1.4 50.0 + - - +
316F LEU* 3.3 1.1 + - - -
317F ALA* 2.8 35.0 + - - +
325F ALA* 3.5 14.3 - - - +
328F ILE* 3.8 10.6 - - - +
329F LEU* 3.9 23.1 - - - -
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Residues in contact with LYS 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A GLU* 3.3 27.7 + - - +
283F LEU* 4.0 18.8 - - + -
284F LYS* 4.7 4.0 - - - +
310F PHE* 2.9 42.0 + - + +
311F ARG* 3.9 6.1 - - - +
312F LYS 3.4 0.2 - - - -
313F GLY* 1.4 71.3 - - - +
315F VAL* 1.4 57.0 + - - +
317F ALA* 3.5 3.1 + - - +
318F GLN* 3.0 54.8 + - - +
329F LEU* 4.2 1.2 - - - +
345F GLU* 3.4 37.7 + - + +
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Residues in contact with VAL 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F LEU* 3.5 27.8 - - + -
288F TYR* 3.6 36.7 - - + +
291F ALA* 4.0 21.8 - - + -
292F LEU* 3.7 17.5 - - + -
295F CYS* 5.4 1.1 - - - -
311F ARG* 3.0 22.5 + - + +
312F LYS* 3.7 5.6 - - - +
314F LYS* 1.4 70.3 - - - +
316F LEU* 1.3 61.8 + - - +
318F GLN* 3.2 5.8 + - - +
319F GLN* 3.0 36.1 + - - +
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Residues in contact with LEU 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292F LEU* 4.2 15.0 - - + -
312F LYS* 2.9 45.9 + - + +
313F GLY 3.8 4.3 - - - +
315F VAL* 1.3 74.7 - - - +
317F ALA* 1.4 56.7 + - - +
319F GLN* 3.5 14.1 + - - +
320F GLY 3.2 4.2 + - - -
321F GLU* 2.8 55.0 + - + +
324F GLU* 3.9 28.7 - - + +
325F ALA* 3.9 10.1 - - + -
328F ILE* 3.9 22.0 - - + -
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Residues in contact with ALA 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313F GLY 2.8 17.7 + - - +
314F LYS* 3.6 9.4 - - - +
316F LEU* 1.4 75.3 - - - +
318F GLN* 1.4 58.7 + - + +
320F GLY 3.2 13.0 + - - -
322F TYR* 3.3 24.6 + - + -
325F ALA* 3.8 6.2 - - + +
329F LEU* 5.0 2.5 - - + -
345F GLU* 4.6 9.4 - - - +
349F LEU* 4.0 25.6 - - + -
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Residues in contact with GLN 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283F LEU* 3.6 10.6 - - - +
286F ASP* 4.8 1.0 - - - +
288F TYR* 3.0 45.7 + - + +
314F LYS* 3.0 51.8 + - + +
315F VAL 3.8 3.8 - - - +
317F ALA* 1.4 77.2 - - + +
319F GLN* 1.3 60.5 + - - +
320F GLY 3.3 0.4 + - - -
345F GLU* 4.9 2.9 + - - +
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Residues in contact with GLN 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F TYR* 3.6 38.1 - - + +
289F ARG* 4.5 10.9 - - - +
292F LEU* 3.3 31.8 - - - +
315F VAL 3.0 19.8 + - - +
316F LEU* 3.7 18.3 - - - +
318F GLN* 1.3 76.5 - - - +
320F GLY* 1.3 58.7 + - - +
321F GLU* 3.6 9.8 - - + +
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Residues in contact with GLY 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316F LEU 3.8 0.2 - - - -
317F ALA 3.2 14.4 + - - -
318F GLN 3.3 1.0 + - - -
319F GLN* 1.3 78.5 - - - +
321F GLU* 1.4 56.7 + - - +
322F TYR* 3.1 35.2 + - - -
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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