Contacts of the helix formed by residues 331 - 339 (chain A) in PDB entry 5M64
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 GLU 331 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A HIS 4.8 1.6 - - - -
107A HIS* 3.2 19.4 + - - +
108A PHE* 2.5 74.8 + - - +
115A VAL* 5.4 4.7 - - + +
327A VAL* 3.0 20.8 + - - +
328A PHE 3.6 3.4 - - - -
330A LYS* 1.3 82.2 - - + +
332A GLN* 1.3 59.4 + - - +
333A CYS* 3.2 5.1 + - - +
334A VAL* 3.3 14.0 - - + +
335A LEU* 2.9 27.1 + - + +
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Residues in contact with GLN 332 (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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328A PHE 2.8 29.4 + - - +
329A ARG* 4.0 13.8 - - - +
330A LYS 3.5 3.0 + - - -
331A GLU* 1.3 75.0 - - - +
333A CYS* 1.3 61.4 + - - +
335A LEU* 3.7 7.6 - - - +
336A GLN* 2.9 68.7 + - + +
349A LEU* 3.5 26.1 - - + +
350A VAL* 3.5 26.6 - - - +
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Residues in contact with CYS 333 (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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116A HIS* 4.7 20.4 - - - -
119A ALA* 4.7 7.6 - - - +
123A ARG* 2.4 46.2 + - - +
331A GLU* 3.2 2.5 - - - +
332A GLN* 1.3 79.2 - - - +
334A VAL* 1.3 59.3 + - - +
336A GLN* 4.3 2.8 + - - +
337A TYR* 4.5 2.3 + - - +
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Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 4.7 11.0 - - + -
115A VAL* 4.4 24.0 - - + +
118A TYR* 5.5 2.2 - - + -
119A ALA* 3.7 31.0 - - + +
122A LEU* 6.3 2.5 - - + -
223A PHE* 6.4 2.7 - - + -
331A GLU* 3.3 30.1 - - + +
333A CYS* 1.3 78.2 - - + +
335A LEU* 1.3 64.2 + - + +
336A GLN 3.3 0.4 - - - -
337A TYR* 3.6 3.1 + - - +
338A VAL* 3.0 33.7 + - + +
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Residues in contact with LEU 335 (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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97A TYR* 5.2 7.9 - - + -
108A PHE* 6.5 0.2 - - + -
328A PHE* 3.5 56.3 - - + +
331A GLU* 2.9 20.2 + - + +
332A GLN* 4.1 7.2 - - - +
334A VAL* 1.3 78.6 - - + +
336A GLN* 1.3 65.1 + - - +
337A TYR 3.2 0.7 + - - -
338A VAL* 3.5 11.6 - - + +
339A PHE* 3.3 53.2 + - + +
350A VAL* 3.7 27.5 - - + +
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Residues in contact with GLN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ARG* 5.2 3.8 - - - +
332A GLN* 2.9 50.8 + - + +
333A CYS* 4.6 4.5 - - - +
334A VAL 3.3 0.6 - - - -
335A LEU* 1.3 76.8 - - - +
337A TYR* 1.3 55.8 + - - +
340A HIS* 2.5 46.7 + - - +
344A ASN* 3.6 12.0 + - - +
347A ARG* 5.5 3.7 - - - -
348A LYS 2.4 34.2 + - - +
349A LEU* 3.6 7.1 - - - +
350A VAL* 3.8 5.5 - - - +
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Residues in contact with TYR 337 (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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119A ALA* 5.6 2.0 - - - +
122A LEU* 3.0 55.4 + - + -
123A ARG* 4.4 24.7 - - - +
125A LEU* 3.7 3.9 - - + +
126A GLN* 3.1 54.3 + - + +
216A ARG* 3.5 28.6 + - - -
333A CYS 4.5 1.2 + - - +
334A VAL* 3.6 6.2 + - - +
335A LEU 3.1 0.2 - - - -
336A GLN* 1.3 78.2 - - - +
338A VAL* 1.3 57.4 + - - +
339A PHE 3.0 5.2 - - - -
340A HIS* 2.7 42.1 + - + +
341A SER 4.3 4.1 + - - -
342A ARG 5.2 4.3 - - - -
343A PRO* 6.0 1.6 - - + -
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Residues in contact with VAL 338 (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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97A TYR* 3.6 24.9 - - + +
122A LEU* 5.2 7.4 - - + +
216A ARG* 4.8 3.5 + - - +
220A VAL* 5.1 11.1 - - + +
223A PHE* 4.7 23.3 - - + -
334A VAL* 3.0 25.8 + - + +
335A LEU* 3.5 28.0 - - + +
337A TYR* 1.3 79.3 - - - +
339A PHE* 1.3 79.4 + - + +
340A HIS 3.5 0.4 - - - -
1627A LEU* 4.8 0.5 - - - +
1628A ASP* 3.9 7.8 - - - +
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Residues in contact with PHE 339 (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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94A LEU* 6.0 0.2 - - - -
97A TYR* 3.6 39.9 - + - -
328A PHE* 4.9 3.8 - + - -
335A LEU* 3.3 39.4 + - + +
337A TYR 3.0 0.6 - - - -
338A VAL* 1.3 90.5 - - + +
340A HIS* 1.3 76.8 + - + +
350A VAL* 4.9 13.7 - - + -
354A SER* 5.8 1.3 - - - -
355A PHE* 3.4 37.5 - + - -
1627A LEU* 3.4 40.6 - - + +
1628A ASP* 3.1 17.1 - - - +
1629A ASN* 4.1 5.5 - - - +
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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