Contacts of the helix formed by residues 309 - 320 (chain D) in PDB entry 4MNE
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 ALA 309 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612C GLN* 4.9 8.5 - - - +
613C LEU* 6.1 2.5 - - + -
625C ILE 5.6 0.2 - - - +
626C ARG 4.9 1.6 - - - +
627C MET* 4.1 32.3 - - + +
307D PRO 4.2 1.4 + - - -
308D MET* 1.3 77.4 - - - +
310D ILE* 1.3 66.0 + - - +
311D PHE* 4.4 4.5 - - + +
312D GLU* 3.1 30.4 + - + +
313D LEU* 3.3 9.4 + - - +
630F LYS* 6.2 1.1 - - - +
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Residues in contact with ILE 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612C GLN* 5.0 5.1 - - - +
613C LEU* 4.9 19.9 - - + +
625C ILE 5.5 0.4 - - - +
663C ASP* 3.8 22.7 - - - +
666C ILE* 4.2 20.2 - - + -
224D VAL* 5.1 5.2 - - + -
225D GLY 4.1 29.2 - - - +
226D THR* 4.3 6.4 + - - -
227D ARG* 3.8 32.5 - - - +
308D MET 3.5 1.8 + - - -
309D ALA* 1.3 72.2 - - - +
311D PHE* 1.3 61.7 - - + +
313D LEU* 3.0 12.6 + - + +
314D LEU* 2.8 40.4 + - + +
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Residues in contact with PHE 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625C ILE* 3.3 39.5 + - + +
626C ARG* 3.6 34.3 - - + +
628C GLN* 4.3 15.0 - - - -
666C ILE* 4.7 0.7 - - + -
667C PHE* 3.5 42.0 - + - -
670C GLY* 3.7 7.6 - - - -
671C ARG* 3.6 40.6 - - - -
309D ALA* 3.2 2.3 - - + +
310D ILE* 1.3 83.0 - - + +
312D GLU* 1.3 65.9 + - - +
314D LEU* 3.3 7.8 + - + +
315D ASP* 3.0 29.0 + - + +
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Residues in contact with GLU 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626C ARG 4.3 3.0 - - - +
627C MET 4.7 4.5 - - - +
628C GLN* 3.4 41.2 + - - +
308D MET* 3.4 31.5 - - + +
309D ALA* 3.1 26.6 + - + +
311D PHE* 1.3 77.6 - - - +
313D LEU* 1.3 50.2 + - - +
315D ASP* 3.0 10.6 + - - +
316D TYR* 2.7 31.4 + - - +
630F LYS* 5.9 0.7 + - - -
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Residues in contact with LEU 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D THR 3.5 24.7 - - - +
227D ARG* 3.8 21.1 - - + -
228D SER 5.6 0.7 - - - +
261D TYR* 4.0 12.6 - - + +
263D ILE* 3.7 32.0 - - + +
308D MET* 3.5 40.8 - - + +
309D ALA 3.5 9.4 - - - +
310D ILE* 3.0 14.1 + - + +
312D GLU* 1.3 72.9 - - - +
314D LEU* 1.3 68.9 + - + +
316D TYR* 3.6 4.5 - - - +
317D ILE* 3.0 29.8 + - + +
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Residues in contact with LEU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663C ASP* 3.3 30.5 - - + +
666C ILE* 3.6 24.5 - - + -
667C PHE* 3.5 26.0 - - + -
228D SER* 3.6 34.3 - - - +
235D LEU* 4.2 16.2 - - + -
310D ILE* 2.8 26.4 + - + +
311D PHE* 3.6 7.9 - - - +
313D LEU* 1.3 78.7 - - + +
315D ASP* 1.3 61.1 + - - +
317D ILE* 3.5 3.9 + - + +
318D VAL* 3.2 29.6 + - - +
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Residues in contact with ASP 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628C GLN* 5.8 2.0 + - - -
667C PHE* 4.0 8.1 - - + -
671C ARG* 3.3 30.6 + - - -
311D PHE* 3.0 24.1 + - + +
312D GLU* 3.4 13.9 - - - +
314D LEU* 1.3 74.6 - - - +
316D TYR* 1.3 66.5 + - - +
318D VAL 4.5 0.2 - - - +
319D ASN* 2.9 48.6 + - - +
320D GLU* 4.7 1.6 - - - +
601F LYS* 5.7 2.8 + - - -
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Residues in contact with TYR 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D ILE* 4.2 28.5 - - + -
264D PRO* 4.0 13.7 - - + -
265D PRO* 3.0 42.2 - - + +
308D MET* 4.3 8.3 - - + -
312D GLU 2.7 12.9 + - - +
313D LEU* 3.2 8.3 + - - +
315D ASP* 1.3 76.7 + - - +
317D ILE* 1.3 64.3 + - - +
318D VAL 3.0 0.2 + - - -
320D GLU* 2.8 67.7 + - + +
321D PRO* 3.1 32.1 + - - +
322D PRO* 5.1 0.4 + - + -
323D PRO* 5.2 4.9 - - + -
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Residues in contact with ILE 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D SER* 4.0 26.7 - - - +
229D TYR* 5.4 0.4 - - - -
230D MET 3.5 26.9 - - - +
232D PRO* 3.9 23.6 - - + +
235D LEU* 3.7 16.8 - - + -
247D TRP* 4.0 15.8 - - + +
251D LEU* 5.4 0.9 - - + -
261D TYR* 4.5 2.7 - - - +
263D ILE* 3.4 28.3 - - + -
313D LEU* 3.0 18.6 + - + +
314D LEU* 3.5 8.3 - - - +
316D TYR* 1.3 79.9 - - - +
318D VAL* 1.3 60.0 + - - +
320D GLU 4.3 1.4 - - - +
344D LYS* 3.6 16.3 - - - +
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Residues in contact with VAL 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667C PHE* 3.8 26.9 - - + -
232D PRO* 4.5 8.0 - - + +
235D LEU* 3.8 28.3 - - + -
236D GLN* 3.3 39.7 + - + +
314D LEU 3.2 17.8 + - - +
315D ASP 3.4 3.1 + - - +
316D TYR 3.1 1.2 - - - -
317D ILE* 1.3 74.6 - - - +
319D ASN* 1.3 70.9 + - - +
344D LYS* 2.9 18.8 + - - -
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Residues in contact with ASN 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667C PHE* 5.0 1.0 - - - -
671C ARG* 4.4 11.1 - - - +
315D ASP* 2.9 45.7 + - - +
318D VAL* 1.3 96.3 - - - +
320D GLU* 1.3 71.5 + - - +
321D PRO* 4.7 1.2 - - - +
344D LYS* 3.4 4.9 - - - +
635F PHE* 5.7 2.6 - - - -
706F LEU* 6.1 5.4 - - + +
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Residues in contact with GLU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D ASP* 4.7 2.1 - - - +
316D TYR* 2.8 70.3 + - + +
317D ILE* 4.3 1.4 - - - +
319D ASN* 1.3 84.1 - - - +
321D PRO* 1.3 75.7 - - + +
344D LYS* 2.5 28.4 + - - +
571F SER* 4.4 12.1 + - - -
601F LYS* 2.7 37.2 + - - +
635F PHE* 4.1 12.6 - - - -
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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