Contacts of the helix formed by residues 311 - 323 (chain B) in PDB entry 4MG5
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 THR 311 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B SER 4.7 3.6 - - - +
310B LEU* 1.3 76.4 - - - +
312B ALA* 1.3 65.7 + - - +
313B ASP* 3.4 8.5 + - - +
314B GLN* 3.1 38.0 + - - +
315B MET* 2.8 21.7 + - - +
481B LYS* 4.4 4.3 - - - +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B THR* 1.3 73.7 - - - +
313B ASP* 1.3 57.0 + - - +
315B MET* 3.2 4.0 + - - +
316B VAL* 2.9 34.6 + - - +
481B LYS* 4.9 4.4 - - - +
484B ASP* 5.2 1.1 - - + +
485B THR* 3.9 18.1 - - - +
488B HIS* 3.3 45.8 - - + +
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B THR* 3.3 7.4 + - - +
312B ALA* 1.3 76.1 - - - +
314B GLN* 1.3 61.6 + - + +
316B VAL* 3.4 8.3 + - - +
317B SER* 2.9 36.0 + - - +
488B HIS* 3.3 23.0 + - - -
489B LEU* 5.6 1.0 - - - +
492B LYS* 3.2 26.2 + - - -
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Residues in contact with GLN 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B SER 4.4 1.6 - - - +
310B LEU* 3.2 31.7 - - + +
311B THR* 3.1 43.0 + - + +
313B ASP* 1.3 78.0 - - + +
315B MET* 1.3 57.2 + - - +
317B SER* 3.4 5.1 + - - -
318B ALA* 2.8 32.8 + - - +
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Residues in contact with MET 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA* 3.7 14.1 - - + +
310B LEU* 4.1 6.9 - - + +
311B THR 2.8 12.2 + - - +
312B ALA* 3.4 9.0 - - - +
314B GLN* 1.3 75.6 - - - +
316B VAL* 1.3 57.4 + - - +
318B ALA* 3.6 3.8 - - - +
319B LEU* 2.9 49.8 + - + +
365B PRO* 3.6 37.7 - - + +
478B VAL* 5.8 3.4 - - + -
481B LYS* 3.3 36.1 - - + +
482B ILE* 5.1 14.1 - - + -
485B THR* 3.6 23.1 - - + +
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ALA 2.9 22.2 + - - +
313B ASP* 3.7 10.3 - - - +
315B MET* 1.3 75.3 - - - +
317B SER* 1.3 59.2 + - - +
319B LEU* 3.2 7.9 + - - +
320B LEU* 2.8 40.7 + - + +
443B GLU* 3.7 33.7 - - + +
446B VAL* 4.9 2.2 - - + +
447B CYS* 5.1 1.3 - - - -
485B THR* 3.4 22.4 - - + -
488B HIS* 5.1 0.7 - - + -
489B LEU* 3.6 24.0 - - + -
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Residues in contact with SER 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ASP* 2.9 21.2 + - - +
314B GLN* 3.8 5.4 - - - -
316B VAL* 1.3 78.4 - - - +
318B ALA* 1.3 58.1 + - - +
320B LEU* 3.3 9.0 + - - +
321B ASP* 2.9 32.3 + - - +
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B LEU* 4.7 5.8 - - + -
314B GLN 2.8 20.1 + - - +
315B MET* 3.6 4.9 - - - +
317B SER* 1.3 76.1 - - - +
319B LEU* 1.3 62.9 + - - +
321B ASP* 3.4 7.0 + - - +
322B ALA* 3.1 24.4 + - - +
363B ARG* 4.7 6.0 + - - +
365B PRO* 4.2 21.3 - - + -
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B MET* 2.9 36.9 + - + +
316B VAL* 3.6 4.7 - - - +
318B ALA* 1.3 75.2 - - - +
320B LEU* 1.3 64.4 + - - +
322B ALA* 3.3 13.3 + - + +
323B GLU* 3.4 16.1 + - - +
360B TRP* 5.0 6.4 + - - +
363B ARG 5.2 0.7 - - - +
364B VAL* 4.3 20.6 - - + -
365B PRO* 3.8 24.9 - - + -
446B VAL* 3.9 27.8 - - + +
447B CYS* 4.1 20.6 - - - -
450B SER* 3.8 24.2 - - - +
482B ILE* 5.3 3.1 - - + -
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B VAL* 2.8 42.3 + - + +
317B SER* 3.7 8.5 - - - +
319B LEU* 1.3 73.9 - - - +
321B ASP* 1.3 61.6 + - - +
323B GLU* 3.3 22.0 - - - +
442B GLY 4.4 6.3 - - - +
443B GLU* 4.2 14.6 - - + +
446B VAL* 4.1 19.1 - - + -
601B GOL 3.9 31.8 + - - +
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Residues in contact with ASP 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B SER 2.9 17.9 + - - +
318B ALA* 3.7 7.0 - - - +
319B LEU 3.2 0.2 - - - -
320B LEU* 1.3 77.1 - - - +
322B ALA* 1.3 61.9 + - - +
323B GLU 3.4 4.7 + - - +
363B ARG* 2.7 34.7 + - - +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ALA 3.1 16.0 + - - +
319B LEU* 3.8 9.0 - - + +
320B LEU 3.2 0.4 - - - -
321B ASP* 1.3 76.2 - - - +
323B GLU* 1.3 67.5 + - - +
324B PRO* 3.2 3.8 - - - +
360B TRP* 3.4 30.7 - - + +
363B ARG* 3.5 47.3 + - + +
364B VAL* 5.6 0.2 - - + -
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Residues in contact with GLU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU 3.4 4.8 + - - +
320B LEU* 3.3 18.3 + - - +
321B ASP 3.2 5.3 - - - +
322B ALA* 1.3 77.8 - - - +
324B PRO* 1.3 77.0 - - - +
325B PRO* 4.6 0.3 - - - +
360B TRP* 4.1 4.5 + - - -
445B PHE* 3.5 13.0 - - - -
446B VAL* 3.7 22.9 - - + +
449B LYS* 2.6 38.0 + - - -
601B GOL 2.9 31.7 + - - +
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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