Contacts of the helix formed by residues 311 - 316 (chain A) in PDB entry 4M8J
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 GLY 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ASN* 5.6 1.6 - - - -
305A ASP* 3.9 3.4 + - - +
309A LYS* 3.4 3.1 - - - +
310A GLY* 1.3 78.6 - - - +
312A PHE* 1.3 64.3 + - - +
313A PRO* 4.7 0.4 - - - +
314A GLN* 3.2 23.2 + - - +
315A ALA* 3.1 26.3 + - - +
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Residues in contact with PHE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TYR 4.7 0.7 - - - -
115A TYR* 3.6 38.6 - + - -
118A SER 3.8 16.2 - - - -
119A PRO 4.0 1.6 - - - +
120A PRO* 3.5 52.9 - - + -
137A TYR* 3.4 37.9 - + - -
303A TYR* 4.5 3.8 - + + -
305A ASP* 5.1 2.0 + - - +
310A GLY* 3.5 3.1 - - - -
311A GLY* 1.3 75.5 - - - +
313A PRO* 1.4 80.4 - - + +
315A ALA* 3.0 5.5 + - - +
316A TRP* 3.0 36.7 + + + +
317A THR* 4.1 5.2 - - - -
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Residues in contact with PRO 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU* 4.5 2.0 - - - +
303A TYR* 3.4 56.8 - - + +
304A THR* 3.7 12.6 - - + +
305A ASP* 4.2 9.2 - - + -
312A PHE* 1.4 94.5 - - + +
314A GLN* 1.3 67.5 + - - +
317A THR* 2.7 43.2 + - - +
318A VAL* 2.8 17.1 + - + -
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Residues in contact with GLN 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 3.9 4.4 - - + -
48A THR* 3.4 42.7 + - - +
49A ASN* 3.1 27.0 + - - +
304A THR* 2.6 40.3 + - - +
305A ASP* 4.9 1.1 + - - +
309A LYS* 6.1 0.2 - - - -
311A GLY* 3.2 31.5 + - - +
313A PRO* 1.3 82.1 - - - +
315A ALA* 1.3 62.6 + - - +
318A VAL* 3.3 27.3 - - + +
319A PHE 4.2 0.7 + - - -
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 4.2 12.6 - - + -
311A GLY 3.1 20.2 + - - +
312A PHE* 3.0 6.3 + - - +
314A GLN* 1.3 79.8 - - - +
316A TRP* 1.3 74.6 + - + +
319A PHE* 3.5 17.4 - - - +
473A GLN* 3.5 15.7 + - - +
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Residues in contact with TRP 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TRP* 3.7 27.1 - + - -
111A GLU* 5.0 2.5 - - + -
114A TYR* 3.4 58.0 + + + +
115A TYR* 3.9 26.2 - + + -
141A HIS* 4.2 8.1 - - + -
312A PHE* 3.0 27.9 + + + +
315A ALA* 1.3 93.7 - - + +
317A THR* 1.3 67.9 + - - +
318A VAL 3.3 1.8 - - - -
319A PHE* 4.0 11.2 - + - +
320A TYR* 3.0 66.1 + + + -
469A LEU* 5.1 4.9 - - + -
473A GLN* 4.6 7.4 - - - -
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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