Contacts of the helix formed by residues 86 - 94 (chain A) in PDB entry 3RU0
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ASP 3.8 4.8 + - - +
83A HIS* 2.7 37.4 + - + +
85A ARG* 1.3 76.0 - - - +
87A CYS* 1.3 66.4 + - - +
88A LYS 3.4 2.9 - - - -
89A CYS* 3.1 9.2 + - - +
90A LEU* 3.0 30.6 + - + +
103A ARG* 2.8 47.9 + - - +
106A GLY* 6.0 4.3 - - - -
107A ARG* 2.9 33.4 + - + +
154A PHE* 5.2 9.0 - - + -
155A MET* 5.5 4.7 - - + -
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Residues in contact with CYS 87 (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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62A CYS* 3.9 1.3 - - - -
64A GLN* 3.5 29.4 - - - -
65A CYS* 3.3 14.2 - - - +
80A TRP* 4.6 8.5 - - + -
83A HIS* 3.0 29.0 + - + +
84A LYS 3.8 9.6 - - - +
85A ARG 3.6 0.4 - - - -
86A GLU* 1.3 77.6 - - - +
88A LYS* 1.3 61.7 + - + +
90A LEU* 3.5 0.6 + - - +
91A LYS* 3.0 24.8 + - - +
439A ZN 2.4 33.4 - - - -
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Residues in contact with LYS 88 (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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84A LYS 4.9 2.7 + - - +
85A ARG 5.0 0.6 + - - -
86A GLU 3.4 0.4 - - - -
87A CYS* 1.3 82.0 - - + +
89A CYS* 1.3 58.5 + - - +
91A LYS* 3.6 24.4 + - - +
92A SER* 3.1 28.4 + - - -
157A GLU* 4.0 34.8 - - + +
158A GLU* 3.9 23.9 + - - +
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Residues in contact with CYS 89 (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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85A ARG 3.8 21.3 - - - -
86A GLU* 3.1 6.0 + - - +
88A LYS* 1.3 74.9 - - - +
90A LEU* 1.3 64.3 + - - +
92A SER* 3.0 19.4 + - - -
93A CYS* 3.5 7.3 + - - +
154A PHE* 3.2 49.5 - - + +
155A MET* 4.0 22.0 - - - -
157A GLU* 5.0 5.4 - - - -
158A GLU* 3.9 17.5 - - - -
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Residues in contact with LEU 90 (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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65A CYS* 4.4 0.9 - - + -
67A VAL* 4.0 28.4 - - + +
68A ALA 4.9 0.4 - - - +
83A HIS* 3.9 17.0 - - + -
86A GLU* 3.0 27.4 + - + +
87A CYS 3.7 3.6 - - - +
89A CYS* 1.3 75.5 - - - +
91A LYS* 1.3 62.4 + - - +
93A CYS* 3.4 7.0 + - - -
94A LYS* 3.2 22.2 + - - +
97A TYR* 3.8 33.4 - - + -
98A PRO* 4.3 1.3 - - + -
103A ARG* 3.8 34.5 - - - +
154A PHE* 3.8 24.7 - - + -
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Residues in contact with LYS 91 (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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64A GLN* 3.1 33.0 - - - +
65A CYS* 3.9 18.1 - - + +
87A CYS* 3.0 17.5 + - - +
88A LYS* 3.6 26.1 - - - +
89A CYS 3.3 0.2 - - - -
90A LEU* 1.3 77.7 - - - +
92A SER* 1.3 63.8 + - - +
93A CYS 3.3 0.5 + - - -
94A LYS* 3.4 16.9 + - - +
341B LEU 2.8 21.8 + - - +
342B GLY* 3.2 34.5 - - - +
343B LEU* 4.0 9.6 - - + +
344B LEU 5.6 1.0 + - - -
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Residues in contact with SER 92 (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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88A LYS 3.1 12.0 + - - -
89A CYS* 3.0 17.3 + - - -
91A LYS* 1.3 80.3 - - - +
93A CYS* 1.3 60.0 + - - +
94A LYS 3.8 0.3 + - - +
154A PHE 5.0 1.2 + - - -
156A ARG* 4.3 26.2 + - - -
157A GLU* 4.3 16.5 + - - +
342B GLY 5.2 4.0 - - - -
344B LEU* 6.5 0.4 - - - -
382B HIS* 3.4 29.5 + - - -
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Residues in contact with CYS 93 (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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89A CYS 3.5 11.6 + - - +
90A LEU* 3.4 15.5 - - - -
91A LYS 3.2 0.4 - - - -
92A SER* 1.3 80.3 + - - +
94A LYS* 1.3 56.9 + - - +
95A PRO* 4.0 0.9 - - - +
96A ARG* 2.7 63.9 + - + +
97A TYR* 4.2 7.6 - - - -
98A PRO* 4.3 0.9 - - - -
153A HIS* 6.5 0.7 - - + -
154A PHE* 3.9 22.9 - - + -
156A ARG* 6.0 2.9 - - - +
382B HIS* 5.5 1.2 - - - -
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Residues in contact with LYS 94 (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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65A CYS 2.8 29.6 + - - -
66A ARG* 3.2 17.7 - - - +
67A VAL* 3.8 16.4 - - + -
90A LEU 3.2 12.4 + - - +
91A LYS* 3.4 15.0 + - - +
92A SER 4.4 3.6 - - - +
93A CYS* 1.3 74.9 - - - +
95A PRO* 1.4 71.9 - - + +
96A ARG 3.6 2.7 + - - -
343B LEU* 3.9 6.9 - - - +
344B LEU* 5.9 0.2 - - - +
345B GLU* 3.3 33.8 + - + +
346B GLU* 2.6 36.8 + - - +
382B HIS* 4.4 10.9 - - - -
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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