Contacts of the helix formed by residues 85 - 93 (chain S) in PDB entry 2X86
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 85 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83S GLU* 2.9 22.3 + - - +
84S TRP* 1.3 74.8 - - - +
86S GLY* 1.3 57.3 + - - +
87S LYS* 2.9 12.4 + - - +
88S TYR* 2.7 33.6 + - + +
89S MET* 2.9 28.8 + - - +
139S VAL* 5.1 0.2 - - - -
34T LYS* 3.3 38.1 + - + +
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Residues in contact with GLY 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84S TRP 3.0 6.3 + - - -
85S ASP* 1.3 70.7 + - - +
87S LYS* 1.3 60.1 + - - +
89S MET* 4.1 1.3 - - - -
90S MET* 2.8 36.6 + - - +
139S VAL* 4.1 22.4 - - - -
33T LEU* 2.8 31.3 + - - -
34T LYS 3.3 0.4 + - - -
36T GLY* 4.1 0.9 - - - -
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Residues in contact with LYS 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85S ASP* 2.9 9.1 + - - +
86S GLY* 1.3 76.3 - - - +
88S TYR* 1.3 62.9 + - - +
90S MET* 4.0 2.7 - - - +
91S ASP* 3.0 45.4 + - - +
32T ASN* 4.3 9.4 - - - +
33T LEU* 3.3 10.8 + - - +
34T LYS* 3.9 21.3 - - + +
50T TYR* 5.9 1.1 - - - -
52T ASP* 3.5 38.6 + - + +
54T GLU* 5.4 5.5 - - - +
55T ASP* 5.4 1.2 + - - -
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Residues in contact with TYR 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53S LYS* 3.0 25.0 + - - -
78S CYS* 3.6 29.6 - - + -
83S GLU* 4.6 13.7 - - + -
85S ASP* 2.7 29.9 + - + +
87S LYS* 1.3 74.7 - - - +
89S MET* 1.3 66.4 + - - +
91S ASP* 3.1 6.7 + - + +
92S ASN* 2.8 52.8 + - + +
400S NAP 3.4 15.8 + - - -
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Residues in contact with MET 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78S CYS* 3.9 16.8 - - - +
80S SER 3.9 10.5 - - - +
83S GLU* 3.4 48.7 - - + +
85S ASP 2.9 15.4 + - - +
86S GLY* 3.3 8.7 + - - +
88S TYR* 1.3 80.6 - - - +
90S MET* 1.3 58.2 + - - +
92S ASN* 5.0 0.9 - - - -
93S ASN* 2.9 60.1 + - - +
139S VAL* 3.8 14.4 - - + +
140S PHE* 3.9 16.2 - - - +
143S SER* 3.6 20.4 - - - +
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Residues in contact with MET 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86S GLY* 2.8 23.6 + - - +
87S LYS* 4.1 2.9 - - - +
89S MET* 1.3 73.0 - - + +
91S ASP* 1.3 58.7 + - - +
94S TYR* 3.2 29.4 + - + +
95S GLN* 2.8 28.9 + - - +
139S VAL* 5.0 3.8 - - - -
142S TYR* 4.1 20.6 - - + -
143S SER* 3.9 22.7 - - - -
146S LEU* 3.7 32.8 - - + -
33T LEU* 3.7 19.3 - - + -
50T TYR* 4.2 29.4 - - + -
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Residues in contact with ASP 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57S LEU* 6.2 0.2 - - - +
87S LYS* 3.0 42.1 + - - +
88S TYR* 3.7 6.2 - - + +
90S MET* 1.3 77.5 - - - +
92S ASN* 1.3 60.7 + - + +
95S GLN* 3.3 18.2 - - - +
96S TYR* 2.9 31.4 + - - +
52T ASP* 5.2 3.9 - - - +
55T ASP* 4.2 14.6 - - - +
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Residues in contact with ASN 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53S LYS* 2.8 29.8 + - - +
74S HIS* 5.7 0.7 + - - -
76S GLY 5.0 0.7 - - - +
77S ALA* 4.9 1.0 - - - -
78S CYS* 3.2 8.5 - - - +
88S TYR* 2.8 47.2 + - + +
89S MET* 4.4 0.4 - - - +
91S ASP* 1.3 76.5 - - + +
93S ASN* 1.3 73.5 + - - +
96S TYR* 3.1 24.3 - - - +
400S NAP 3.0 34.9 + - - -
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Residues in contact with ASN 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74S HIS* 6.2 0.2 - - - -
77S ALA* 3.4 13.4 - - + +
78S CYS* 2.8 46.9 + - - +
89S MET* 2.9 28.8 + - - +
92S ASN* 1.3 83.0 + - - +
94S TYR* 1.3 63.9 + - - +
97S SER* 2.8 32.7 + - - -
140S PHE* 4.0 7.9 - - - -
143S SER* 3.2 28.6 + - - +
144S LYS* 4.6 6.9 - - + +
147S PHE* 6.0 0.4 - - - -
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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