Contacts of the helix formed by residues 85 - 93 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83K GLU* 2.9 22.6 + - - +
84K TRP* 1.3 74.4 - - - +
86K GLY* 1.3 57.1 + - - +
87K LYS* 2.9 12.0 + - - +
88K TYR* 2.7 34.0 + - + +
89K MET* 2.9 25.8 + - - +
139K VAL* 5.1 0.4 - - - -
34L LYS* 3.3 37.6 + - - +
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Residues in contact with GLY 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K TRP 3.0 8.5 + - - -
85K ASP* 1.3 70.4 + - - +
87K LYS* 1.3 60.6 + - - +
89K MET* 4.1 1.1 - - - -
90K MET* 2.8 36.0 + - - +
139K VAL* 4.1 16.8 - - - -
33L LEU* 2.9 25.7 + - - -
34L LYS 3.3 0.6 + - - -
36L GLY* 4.1 9.4 - - - -
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Residues in contact with LYS 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85K ASP* 2.9 8.4 + - - +
86K GLY* 1.3 76.2 - - - +
88K TYR* 1.3 61.8 + - - +
90K MET* 3.9 2.3 - - - +
91K ASP* 3.0 44.7 + - - +
32L ASN* 4.4 9.0 - - - +
33L LEU* 3.3 11.5 + - - +
34L LYS* 3.9 22.0 - - + +
50L TYR* 6.4 0.7 - - - -
52L ASP* 3.7 36.8 + - + +
54L GLU* 5.5 4.5 - - - +
55L ASP* 5.6 1.0 + - - -
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Residues in contact with TYR 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K LYS* 3.0 25.0 + - - -
78K CYS* 3.6 30.1 - - + -
83K GLU* 4.6 14.1 - - + -
85K ASP* 2.7 29.9 + - + +
87K LYS* 1.3 74.0 - - - +
89K MET* 1.3 68.2 + - - +
91K ASP* 3.1 6.3 + - + +
92K ASN* 2.8 53.6 + - + +
400K NAP 3.6 15.4 + - - -
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Residues in contact with MET 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78K CYS* 3.9 15.9 - - - +
80K SER 3.9 10.8 - - - +
83K GLU* 3.4 48.5 - - + +
85K ASP 2.9 15.3 + - - +
86K GLY* 3.3 8.7 + - - +
88K TYR* 1.3 79.1 - - - +
90K MET* 1.3 57.5 + - - +
92K ASN* 5.0 0.4 - - - -
93K ASN* 2.9 60.6 + - - +
139K VAL* 3.8 13.2 - - + +
140K PHE* 3.9 16.2 - - - +
143K SER* 3.6 20.4 - - - +
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Residues in contact with MET 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K GLY* 2.8 24.5 + - - +
87K LYS* 4.1 2.7 - - - +
89K MET* 1.3 72.5 - - + +
91K ASP* 1.3 58.4 + - - +
94K TYR* 3.2 30.3 + - + +
95K GLN* 2.8 29.4 + - - +
139K VAL* 5.0 4.5 - - + -
142K TYR* 4.1 21.1 - - + -
143K SER* 3.9 22.9 - - - -
146K LEU* 3.6 32.5 - - + -
33L LEU* 3.7 20.0 - - + -
50L TYR* 4.2 29.2 - - + -
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Residues in contact with ASP 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57K LEU* 6.1 0.2 - - - +
87K LYS* 3.0 41.3 + - - +
88K TYR* 3.7 6.6 - - + +
90K MET* 1.3 78.3 - - - +
92K ASN* 1.3 59.0 + - + +
95K GLN* 3.3 18.7 - - - +
96K TYR* 2.9 31.5 + - - +
52L ASP* 5.2 4.3 - - - +
55L ASP* 4.2 14.8 - - - +
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Residues in contact with ASN 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K LYS* 2.8 29.5 + - - +
74K HIS* 5.7 0.5 + - - -
76K GLY 5.0 0.9 - - - +
77K ALA* 4.9 1.2 - - - -
78K CYS* 3.2 8.3 - - - +
88K TYR* 2.8 47.6 + - + +
89K MET 4.4 0.7 - - - +
91K ASP* 1.3 76.1 - - + +
93K ASN* 1.3 72.7 + - - +
96K TYR* 3.1 23.4 - - - +
400K NAP 3.0 35.2 + - - -
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Residues in contact with ASN 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76K GLY 5.7 0.7 - - - -
77K ALA* 3.4 12.3 - - + +
78K CYS* 2.8 45.6 + - - -
89K MET* 2.9 28.8 + - - +
92K ASN* 1.3 83.3 + - - +
94K TYR* 1.3 64.4 + - - +
97K SER* 2.8 33.6 + - - -
140K PHE* 4.0 7.7 - - - -
143K SER* 3.2 28.2 + - - +
144K LYS* 4.6 7.1 - - + +
147K 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