Contacts of the helix formed by residues 305 - 314 (chain C) in PDB entry 3MGV
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 SER 305 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303C GLY 3.4 4.3 + - - -
304C VAL* 1.3 77.6 - - - +
306C ILE* 1.3 64.7 + - - +
307C PRO* 3.2 18.0 - - - +
308C GLU* 3.1 21.3 + - - +
309C ILE* 3.0 18.5 + - - +
300D ALA* 3.6 9.7 + - - -
303D GLY* 4.1 26.1 - - - -
304D VAL 5.1 1.6 + - - -
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Residues in contact with ILE 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C VAL 5.4 0.7 - - - +
305C SER* 1.3 71.6 - - - +
307C PRO* 1.4 63.9 - - + +
309C ILE* 3.2 10.8 + - + +
310C MET* 2.9 56.0 + - + +
318C VAL* 4.5 17.5 - - + -
321C VAL* 4.8 9.6 - - + -
322C MET* 4.0 25.1 - - + -
325C ILE* 4.6 12.8 - - + -
331C GLU* 4.8 12.1 - - - +
306D ILE* 4.8 6.7 - - + -
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Residues in contact with PRO 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C SER* 3.2 16.8 - - - +
306C ILE* 1.4 95.0 - - + +
308C GLU* 1.3 55.2 + - - +
310C MET* 3.1 17.4 - - + +
311C GLN* 3.1 23.4 + - - +
300D ALA* 4.9 6.3 - - + -
304D VAL 5.0 5.2 - - - +
306D ILE* 3.7 30.7 - - + +
309D ILE* 4.9 12.1 - - + -
321D VAL* 5.4 2.5 - - + -
322D MET* 3.7 9.2 - - - +
325D ILE* 3.9 23.3 - - + +
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Residues in contact with GLU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C MET* 5.0 0.4 - - - +
304C VAL* 3.5 17.0 - - + +
305C SER* 3.1 25.0 + - - +
307C PRO* 1.3 78.8 - - - +
309C ILE* 1.3 64.9 + - - +
311C GLN* 3.5 3.3 + - - +
312C ALA* 3.1 24.7 + - - +
300D ALA* 3.2 31.0 - - + +
301D ARG* 3.1 42.3 + - - +
303D GLY* 4.9 1.2 + - - -
328D LEU* 4.5 15.2 - - + +
334D ALA* 4.9 5.4 - - + +
337D ARG* 3.9 13.4 + - - -
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Residues in contact with ILE 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ALA* 3.8 28.9 - - + +
299C MET* 3.7 24.8 - - + +
300C ALA* 3.6 34.5 - - + +
304C VAL* 3.6 18.8 - - + +
305C SER 3.0 16.0 + - - +
306C ILE* 3.2 11.9 + - + +
308C GLU* 1.3 75.0 - - - +
310C MET* 1.3 63.1 + - - +
312C ALA* 3.3 4.3 + - - +
313C GLY 3.2 17.2 + - - -
315C TRP* 3.6 7.0 - - + -
321C VAL* 3.9 21.5 - - + -
325C ILE* 4.7 10.1 - - + -
331C GLU* 5.5 0.4 - - - +
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Residues in contact with MET 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C ILE* 2.9 24.3 + - + +
307C PRO* 3.1 37.9 - - + +
308C GLU 3.2 0.2 - - - -
309C ILE* 1.3 77.1 - - - +
311C GLN* 1.3 56.6 + - - +
313C GLY 3.5 0.7 + - - -
314C GLY 2.8 6.8 + - - -
315C TRP* 2.6 54.5 + - + +
316C THR 5.0 1.3 - - - -
317C ASN 4.6 2.7 - - - -
318C VAL* 3.8 38.4 - - + -
321C VAL* 3.7 20.4 - - + -
306D ILE* 4.4 2.2 - - + -
318D VAL* 4.3 10.3 - - + -
322D MET* 3.8 16.8 - - + +
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Residues in contact with GLN 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C THR* 3.7 11.2 - - - +
207C ALA* 3.5 23.2 + - - +
208C GLY* 4.8 0.2 - - - -
307C PRO 3.1 10.2 + - - +
308C GLU 4.4 4.2 - - - +
310C MET* 1.3 72.5 - - - +
312C ALA* 1.3 78.4 + - - +
314C GLY* 3.3 8.1 + - - +
301D ARG* 5.0 3.1 + - - -
322D MET* 3.5 20.3 - - + +
325D ILE* 3.7 9.2 - - + +
326D ARG* 2.9 26.8 + - - -
328D LEU* 3.4 48.5 + - + +
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Residues in contact with ALA 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C THR 3.7 4.2 - - - +
171C LEU* 3.7 10.6 - - + +
211C LYS* 2.6 30.7 + - - +
299C MET* 3.8 26.0 - - + -
308C GLU 3.1 19.2 + - - +
309C ILE 3.3 6.0 + - - +
311C GLN* 1.3 86.6 + - - +
313C GLY* 1.3 55.4 + - - +
334D ALA* 5.6 3.4 - - + +
335D MET* 4.9 4.9 - - + -
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Residues in contact with GLY 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C LEU* 3.7 18.6 - - - +
173C ARG* 4.6 1.4 + - - -
207C ALA* 4.6 4.4 - - - +
211C LYS* 5.1 0.2 - - - -
292C ARG* 2.5 30.4 + - - -
309C ILE 3.2 7.7 + - - -
312C ALA* 1.3 78.3 - - - +
314C GLY* 1.3 58.8 + - - +
315C TRP* 3.4 24.6 - - - -
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Residues in contact with GLY 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ARG* 4.3 12.4 + - - -
206C THR* 2.8 28.8 + - - -
207C ALA* 3.7 21.5 - - - +
292C ARG* 4.8 0.4 - - - -
310C MET 2.8 6.3 + - - -
311C GLN 3.3 6.0 + - - -
313C GLY* 1.3 78.9 - - - +
315C TRP* 1.3 62.1 + - - +
316C THR 4.0 0.5 + - - -
1M C 4.1 8.1 + - - -
2M A 4.5 2.6 + - - -
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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
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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