Contacts of the helix formed by residues 76 - 85 (chain A) in PDB entry 5JQE
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 HIS 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A TRP 4.5 0.2 - - - -
75A ALA* 1.3 73.6 - - - +
77A ASP* 1.3 73.1 + - - +
79A PHE* 3.0 25.0 + - + +
108A ALA* 3.5 38.5 - - + +
109A VAL* 4.8 1.3 - - + -
271A VAL 3.2 26.9 - - - -
272A GLY* 3.8 4.0 - - - -
273A VAL* 2.9 43.6 + - + +
275A SER* 3.8 13.9 - - - +
341A ILE* 3.8 5.5 - - + +
342A MET* 2.7 35.1 + - + +
344A ASN* 3.6 15.7 + - + +
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Residues in contact with ASP 77 (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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74A TRP* 5.8 0.3 + - - -
75A ALA* 3.4 21.2 - - - +
76A HIS* 1.3 89.9 + - + +
78A ARG* 1.3 74.6 + - - +
81A GLY 4.6 0.9 + - - -
272A GLY* 5.6 1.4 - - - -
342A MET* 4.3 26.5 - - + +
343A PRO 4.1 14.4 - - - +
344A ASN* 3.3 33.0 - - - +
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Residues in contact with ARG 78 (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* 3.7 39.8 + - - +
57A GLU* 4.5 9.1 + - - +
60A PRO* 4.8 6.3 - - - +
74A TRP* 3.8 28.3 - - + +
75A ALA 3.5 1.1 + - - +
76A HIS 3.1 0.6 - - - -
77A ASP* 1.3 82.3 - - - +
79A PHE* 1.3 65.8 + - - +
80A GLY 3.0 4.7 + - - -
81A GLY* 3.1 13.3 + - - -
82A TYR* 3.4 39.1 + - + +
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Residues in contact with PHE 79 (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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72A ILE* 3.3 31.2 - - + -
74A TRP* 3.5 26.9 - - + -
75A ALA 3.9 8.5 - - - -
76A HIS* 3.0 13.1 + - + +
78A ARG* 1.3 78.5 - - + +
80A GLY* 1.3 61.2 + - - +
82A TYR* 3.4 28.8 + + - -
83A ALA* 3.0 23.7 + - - +
88A LEU* 3.6 15.2 - - + +
109A VAL* 5.7 2.5 - - + -
116A ILE* 4.8 5.9 - - + +
117A ALA* 3.5 23.6 - - + -
275A SER* 3.4 28.5 - - - -
277A GLY* 3.5 17.0 - - - -
344A ASN* 5.6 1.3 - - - +
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Residues in contact with GLY 80 (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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76A HIS 3.8 3.0 + - - -
77A ASP 3.7 4.0 + - - -
78A ARG 3.0 2.0 + - - -
79A PHE* 1.3 77.2 - - - +
81A GLY* 1.3 56.4 + - - +
83A ALA* 3.1 4.0 + - - +
84A GLN* 2.7 30.9 + - - +
111A TYR* 3.8 21.8 - - - -
344A ASN* 3.3 27.5 + - - +
346A PRO* 5.9 1.1 - - - -
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Residues in contact with GLY 81 (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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77A ASP 4.6 0.8 + - - -
78A ARG* 3.1 10.0 + - - -
80A GLY* 1.3 74.8 - - - +
82A TYR* 1.3 66.2 + - - +
84A GLN* 3.4 10.6 + - - +
85A SER* 3.3 23.6 + - - -
87A LEU* 5.2 0.2 - - - +
344A ASN 4.1 3.6 + - - -
346A PRO* 5.6 8.8 - - - +
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Residues in contact with TYR 82 (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* 2.8 34.1 + - - +
59A PHE* 3.6 28.2 - + + +
60A PRO* 3.5 31.0 - - + -
72A ILE* 4.8 6.1 - - + +
74A TRP* 5.0 2.7 - - + -
78A ARG* 3.4 33.6 + - + +
79A PHE* 3.4 38.3 + + - +
80A GLY 3.2 0.4 - - - -
81A GLY* 1.3 77.1 - - - +
83A ALA* 1.3 61.6 + - - +
85A SER 3.3 2.6 + - - -
86A GLY 3.2 3.6 + - - -
87A LEU* 2.8 43.3 + - + +
88A LEU* 3.5 19.7 - - + -
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Residues in contact with ALA 83 (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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79A PHE 3.0 17.3 + - - +
80A GLY* 3.6 3.8 - - - +
82A TYR* 1.3 70.8 - - - +
84A GLN* 1.3 59.8 + - - +
85A SER 3.0 2.2 - - - -
86A GLY* 2.6 25.3 + - - +
87A LEU 4.4 3.1 - - - +
88A LEU* 4.2 5.5 - - + +
111A TYR* 4.1 27.6 - - + -
114A LYS* 5.7 4.8 + - - +
116A ILE* 4.1 25.6 - - + -
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Residues in contact with GLN 84 (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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80A GLY 2.7 20.5 + - - +
81A GLY* 3.5 13.0 - - - +
83A ALA* 1.3 71.7 - - - +
85A SER* 1.3 61.1 + - - +
86A GLY 3.4 0.6 + - - -
111A TYR* 3.1 34.5 + - - +
346A PRO* 5.8 7.7 - - + +
1008A TYR* 5.3 6.5 + - - -
1012A GLU* 6.0 0.2 + - - -
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Residues in contact with SER 85 (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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81A GLY 3.3 10.4 + - - -
82A TYR 3.3 7.8 + - - -
83A ALA 3.0 0.4 - - - -
84A GLN* 1.3 81.2 - - - +
86A GLY* 1.3 63.0 + - - +
87A LEU* 3.3 25.0 + - - +
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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