Contacts of the helix formed by residues 78 - 93 (chain q) in PDB entry 3J7Y
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 SER 78 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290M LEU* 5.2 3.7 - - - +
38g PHE* 5.9 9.8 - - - -
73q GLY 6.0 1.1 - - - -
76q TRP* 3.0 8.1 + - - +
77q PRO* 1.3 85.0 + - - +
79q PRO* 1.4 69.7 - - - +
80q GLU* 4.6 1.2 + - - +
81q GLN* 3.2 17.9 + - - +
82q LEU* 2.8 34.8 + - - +
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Residues in contact with PRO 79 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38g PHE* 6.2 3.4 - - + -
78q SER* 1.4 91.6 - - - +
80q GLU* 1.3 72.9 + - + +
82q LEU* 3.4 7.8 + - + +
83q ARG* 3.0 36.0 + - - +
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Residues in contact with GLU 80 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78q SER* 3.5 1.5 + - - +
79q PRO* 1.3 85.6 - - + +
81q GLN* 1.3 62.4 + - + +
83q ARG* 3.2 23.5 + - - +
84q GLU* 2.9 41.5 + - - +
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Residues in contact with GLN 81 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77q PRO* 3.2 32.4 - - + +
78q SER* 3.2 10.3 + - - +
80q GLU* 1.3 80.0 - - + +
82q LEU* 1.3 57.0 - - - +
84q GLU* 3.2 15.3 + - - +
85q LEU* 2.9 35.7 + - + +
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Residues in contact with LEU 82 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289M ASN* 5.0 14.8 - - + +
290M LEU* 3.7 28.9 - - + +
293M TYR* 3.5 49.4 - - + -
77q PRO* 3.9 16.4 - - + +
78q SER 2.8 24.4 + - - +
79q PRO* 3.5 7.9 - - + +
81q GLN* 1.3 72.2 - - - +
83q ARG* 1.3 62.7 + - - +
85q LEU* 3.2 7.0 + - + +
86q GLU* 2.9 35.3 + - + +
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Residues in contact with ARG 83 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289M ASN* 6.2 0.2 - - - +
79q PRO* 3.0 26.6 + - - +
80q GLU* 3.4 25.7 + - - +
82q LEU* 1.3 82.7 - - + +
84q GLU* 1.3 57.9 + - + +
86q GLU* 3.2 16.0 + - - +
87q ALA* 2.9 29.3 + - + +
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Residues in contact with GLU 84 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X LYS* 5.0 10.9 + - - +
80q GLU* 2.9 35.3 + - - +
81q GLN* 3.4 14.3 + - - +
83q ARG* 1.3 78.4 - - + +
85q LEU* 1.3 57.0 + - + +
87q ALA* 3.2 8.9 + - - +
88q GLU* 2.9 30.3 + - - +
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Residues in contact with LEU 85 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293M TYR* 3.6 30.3 - - + +
77q PRO* 4.0 24.9 - - + -
81q GLN* 2.9 19.6 + - + +
82q LEU* 3.2 10.1 + - - +
84q GLU* 1.3 75.0 - - + +
86q GLU* 1.3 57.5 + - - +
88q GLU* 3.2 15.9 + - + +
89q GLU* 2.9 31.2 + - - +
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Residues in contact with GLU 86 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293M TYR* 4.5 23.2 - - + +
296M SER* 5.7 0.5 + - - -
82q LEU* 2.9 21.8 + - + +
83q ARG* 3.2 20.8 + - - +
85q LEU* 1.3 75.7 - - - +
87q ALA* 1.3 57.2 + - - +
89q GLU* 3.2 8.9 + - + +
90q ARG* 2.9 65.6 + - + +
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Residues in contact with ALA 87 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83q ARG* 2.9 13.6 + - + +
84q GLU* 3.3 12.8 - - - +
86q GLU* 1.3 77.3 - - - +
88q GLU* 1.3 55.9 + - - +
90q ARG* 3.2 13.4 + - - +
91q GLU* 2.9 29.3 + - - +
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Residues in contact with GLU 88 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X LYS* 5.5 4.7 - - - +
50X PHE* 3.2 34.1 - - - -
59X ARG* 4.0 7.2 + - - +
84q GLU 2.9 14.1 + - - +
85q LEU* 3.4 19.4 - - + +
87q ALA* 1.3 75.5 - - - +
89q GLU* 1.3 65.8 + - - +
91q GLU* 3.2 8.5 + - - +
92q TRP* 3.0 34.7 + - + +
93q TYR* 4.6 5.5 - - + -
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Residues in contact with GLU 89 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202M LYS* 3.3 34.0 - - - +
204M MET* 3.3 27.5 - - + +
263M ARG* 5.1 2.2 - - - +
293M TYR* 5.3 5.7 + - + -
85q LEU 2.9 14.9 + - - +
86q GLU* 3.3 13.0 - - + +
88q GLU* 1.3 78.8 - - - +
90q ARG* 1.3 58.4 + - + +
93q TYR* 2.6 65.8 + - + +
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Residues in contact with ARG 90 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86q GLU* 2.9 47.3 + - + +
87q ALA* 3.2 11.9 + - - +
89q GLU* 1.3 78.9 - - + +
91q GLU* 1.3 62.4 + - - +
93q TYR 4.4 5.7 + - - -
94q PRO* 4.9 6.5 - - - +
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Residues in contact with GLU 91 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87q ALA 2.9 12.6 + - - +
88q GLU* 3.2 11.6 + - - +
90q ARG* 1.3 80.4 - - - +
92q TRP* 1.3 103.7 + - + +
94q PRO* 5.4 1.6 - - - +
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Residues in contact with TRP 92 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X ALA* 5.8 1.8 - - + -
50X PHE* 3.5 44.6 - - + +
51X LYS* 4.7 3.4 - - - -
52X ILE* 3.4 38.1 - - + -
59X ARG* 3.2 38.2 - - + +
88q GLU* 3.0 26.7 + - + +
91q GLU* 1.3 110.5 - - + +
93q TYR* 1.3 81.9 + - + +
94q PRO* 3.6 11.0 - - - +
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Residues in contact with TYR 93 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180M ASP* 4.6 7.0 - - - -
204M MET* 3.8 51.7 - - + +
263M ARG* 5.7 1.4 + - - -
59X ARG* 4.0 22.7 + - - -
88q GLU* 4.6 5.2 - - + -
89q GLU* 2.6 52.1 + - + +
90q ARG* 5.0 0.9 - - - -
91q GLU 3.9 0.4 - - - -
92q TRP* 1.3 92.3 - + + +
94q PRO* 1.3 67.1 - - - +
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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