Contacts of the helix formed by residues 78 - 86 (chain B) in PDB entry 5MJ3
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 ASP 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A ALA* 3.7 15.8 - - + +
74B GLY* 6.0 0.9 - - - -
76B GLY* 3.7 14.2 + - - -
77B CYS* 1.3 81.1 + - - +
79B PRO* 1.3 76.0 - - + +
80B GLN* 3.4 14.9 + - - +
81B GLY* 3.0 32.9 + - - -
82B LEU* 3.0 11.4 + - - +
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Residues in contact with PRO 79 (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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201A ALA* 4.3 7.2 - - + -
265A PRO* 3.7 30.5 - - + -
268A TYR* 3.9 25.8 - - + -
269A PHE* 5.0 3.8 - - + -
77B CYS 3.9 0.2 - - - -
78B ASP* 1.3 86.3 - - + +
80B GLN* 1.3 61.8 + - - +
82B LEU* 3.3 5.5 + - + +
83B ARG* 3.0 22.2 + - - +
182B HIS* 3.6 29.8 + - + +
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Residues in contact with GLN 80 (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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78B ASP* 3.2 12.5 + - - +
79B PRO* 1.3 78.5 - - - +
81B GLY* 1.3 63.0 + - - +
83B ARG* 3.2 10.1 + - + +
84B ASP* 3.0 36.5 + - - +
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Residues in contact with GLY 81 (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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76B GLY* 3.6 18.1 - - - -
78B ASP* 3.0 17.8 + - - -
80B GLN* 1.3 79.5 - - - +
82B LEU* 1.3 57.1 + - - +
84B ASP* 3.8 7.4 - - - +
85B ASN 2.9 33.6 + - - +
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Residues in contact with LEU 82 (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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268A TYR* 4.1 9.6 - - + -
30B TRP* 5.1 3.4 - - + -
76B GLY 3.9 1.3 - - - +
77B CYS 3.9 15.7 - - - +
78B ASP 3.0 14.3 + - - +
79B PRO* 3.6 6.1 - - + +
81B GLY* 1.3 74.0 - - - +
83B ARG* 1.3 66.1 + - - +
86B SER* 3.5 28.8 + - - +
89B CYS* 3.7 30.7 - - + -
90B LEU* 5.3 0.4 - - + -
179B VAL* 3.8 32.1 - - + +
182B HIS* 4.0 24.0 - - + -
183B GLY* 5.2 1.3 - - - +
187B LEU* 3.4 27.0 - - + +
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Residues in contact with ARG 83 (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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79B PRO 3.0 13.1 + - - +
80B GLN* 3.6 12.8 - - - +
82B LEU* 1.3 78.0 - - - +
84B ASP* 1.3 69.4 + - - +
85B ASN* 4.7 0.2 - - - -
182B HIS* 5.9 1.3 + - - +
187B LEU* 4.6 15.3 - - + +
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Residues in contact with ASP 84 (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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80B GLN* 3.0 35.5 + - - +
81B GLY* 3.3 7.1 + - - +
83B ARG* 1.3 87.3 - - - +
85B ASN* 1.3 66.2 + - + +
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Residues in contact with ASN 85 (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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76B GLY* 5.1 1.2 - - - +
81B GLY 2.9 14.0 + - - +
82B LEU 4.3 0.4 - - - -
83B ARG 3.5 0.4 - - - -
84B ASP* 1.3 82.5 - - + +
86B SER* 1.3 63.9 + - - +
87B GLN* 3.0 31.0 + - - +
88B PHE* 3.6 41.9 + - + +
89B CYS 4.7 0.5 + - - -
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Residues in contact with SER 86 (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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27B SER* 4.9 9.0 - - - -
30B TRP* 3.8 28.9 - - - -
82B LEU* 3.5 41.2 + - - +
85B ASN* 1.3 71.8 + - - +
87B GLN* 1.3 66.7 + - - +
88B PHE 3.2 0.7 - - - -
89B CYS* 3.3 5.2 + - - +
90B LEU* 3.1 28.7 + - - +
187B LEU* 4.3 2.8 - - - +
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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