Contacts of the helix formed by residues 93 - 108 (chain T) 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 ASN 93 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74T HIS* 6.2 0.2 - - - -
77T ALA* 3.4 12.2 - - + +
78T CYS* 2.8 46.1 + - - +
89T MET* 2.8 28.7 + - - +
92T ASN* 1.3 82.7 + - - +
94T TYR* 1.3 64.1 + - - +
97T SER* 2.8 33.5 + - - -
140T PHE* 4.0 8.1 - - - -
143T SER* 3.2 27.8 + - - +
144T LYS* 4.6 7.2 - - + +
147T PHE* 6.0 0.4 - - - -
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Residues in contact with TYR 94 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48P ALA 4.3 0.9 + - - -
49P ASP* 2.3 42.7 + - - -
50P TYR* 3.6 18.6 - + + -
89T MET 3.7 0.6 + - - -
90T MET* 3.2 38.0 + - + +
93T ASN* 1.3 75.4 - - - +
95T GLN* 1.3 73.4 + - - +
97T SER* 3.2 6.1 + - - -
98T LYS* 2.9 39.6 + - + +
143T SER* 4.1 9.6 - - - +
146T LEU* 3.5 42.6 - - + +
147T PHE* 3.6 28.2 - + + -
150T TYR* 3.7 16.0 - - + +
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Residues in contact with GLN 95 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50P TYR 4.0 10.0 - - - +
51P MET* 5.4 6.6 - - - +
55P ASP* 5.6 4.0 - - - +
90T MET 2.8 15.0 + - - +
91T ASP* 3.3 26.9 - - - +
94T TYR* 1.3 76.7 - - + +
96T TYR* 1.3 64.3 + - - +
98T LYS* 3.0 42.6 + - - +
99T GLU* 3.0 47.1 + - - +
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Residues in contact with TYR 96 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5T THR* 5.4 0.9 - - + -
30T VAL* 4.1 0.2 - - - +
53T LYS* 2.7 41.3 + - + +
54T GLU* 5.5 1.6 - - - -
56T PHE* 3.5 18.4 - + - -
57T LEU* 3.6 37.1 + - + -
74T HIS* 3.9 16.6 - + - +
91T ASP 2.9 12.8 + - - +
92T ASN* 3.1 26.9 - - - +
94T TYR 3.3 0.4 - - - -
95T GLN* 1.3 73.6 - - - +
97T SER* 1.3 64.6 + - - +
99T GLU* 3.0 17.2 + - - +
100T LEU* 3.0 31.8 + - + +
400T NAP 3.5 35.0 + + - -
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Residues in contact with SER 97 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74T HIS* 2.8 32.5 + - - -
76T GLY 5.2 0.2 + - - -
93T ASN* 2.8 21.5 + - - -
94T TYR 3.5 3.8 - - - -
96T TYR* 1.3 80.6 - - - +
98T LYS* 1.3 62.9 + - - +
100T LEU* 3.3 3.3 + - - +
101T LEU* 2.9 24.6 + - - +
111T PHE* 4.1 1.0 - - - -
113T TYR* 5.9 0.3 - - - -
144T LYS* 5.7 3.5 + - - -
147T PHE* 3.6 33.1 - - - -
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Residues in contact with LYS 98 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P ASP* 2.9 31.8 + - - +
50P TYR 4.1 2.8 + - - -
51P MET* 5.0 5.7 - - - +
94T TYR* 2.9 29.8 + - + +
95T GLN* 3.0 44.8 + - - +
97T SER* 1.3 76.2 - - - +
99T GLU* 1.3 65.2 + - - +
101T LEU* 3.2 3.2 + - - +
102T HIS* 3.0 36.5 + - + +
147T PHE* 3.5 12.1 - - + -
150T TYR* 3.6 46.1 + - + +
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Residues in contact with GLU 99 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57T LEU* 4.0 14.8 - - + -
60T ILE* 3.9 8.3 - - + +
61T MET* 3.4 44.1 - - + +
95T GLN* 3.0 38.2 + - - +
96T TYR 3.2 9.2 - - - +
98T LYS* 1.3 80.4 - - - +
100T LEU* 1.3 61.8 + - - +
102T HIS* 3.4 7.8 + - - +
103T TYR* 3.2 22.0 + - - +
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Residues in contact with LEU 100 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5T THR* 4.1 13.7 - - + -
56T PHE* 3.7 24.7 - - + -
57T LEU* 5.2 2.5 - - + -
60T ILE* 3.9 18.2 - - + -
72T ILE* 4.4 12.8 - - + -
74T HIS* 3.3 46.7 - - + +
96T TYR* 3.0 23.8 + - + +
97T SER 3.6 7.4 - - - +
99T GLU* 1.3 74.7 - - - +
101T LEU* 1.3 67.1 + - - +
103T TYR* 3.1 7.3 + - + +
104T CYS* 2.9 26.0 + - - -
111T PHE* 3.7 12.8 - - + -
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Residues in contact with LEU 101 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97T SER 2.9 17.4 + - - +
98T LYS 3.5 3.8 - - - +
100T LEU* 1.3 76.5 - - - +
102T HIS* 1.3 59.7 + - + +
104T CYS* 3.3 1.4 + - - +
105T LEU* 2.8 42.0 + - + +
111T PHE* 3.8 31.1 - - + -
147T PHE* 4.0 21.1 - - + -
150T TYR* 4.0 28.9 - - + -
151T VAL* 4.3 9.4 - - + -
154T ILE* 4.3 13.5 - - + -
162T ILE* 3.8 28.9 - - + -
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Residues in contact with HIS 102 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98T LYS* 3.0 34.7 + - + +
99T GLU* 3.9 8.3 - - - +
100T LEU 3.2 0.2 - - - -
101T LEU* 1.3 77.3 - - + +
103T TYR* 1.3 64.0 + - - +
105T LEU* 3.3 12.8 + - + +
106T GLU* 3.0 30.4 + - - +
150T TYR* 2.6 39.0 + + - -
154T ILE* 4.5 14.4 - - + -
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Residues in contact with TYR 103 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3T ILE* 6.0 0.4 - - + -
60T ILE* 3.5 59.0 - - + -
63T GLY* 4.3 1.1 - - - -
64T GLU 2.6 28.6 + - - -
65T GLU* 3.8 5.4 + - - -
66T PHE* 3.3 17.4 + + - -
69T VAL* 5.6 3.1 - - + +
72T ILE* 4.7 7.2 - - + -
99T GLU 3.2 12.5 + - - +
100T LEU* 3.1 9.1 + - - +
102T HIS* 1.3 78.1 - - - +
104T CYS* 1.3 71.8 + - - +
106T GLU* 3.6 1.3 + - - -
107T ARG* 3.1 79.3 + - - +
109T ILE* 4.1 12.7 - - + +
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Residues in contact with CYS 104 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72T ILE* 3.4 36.1 - - - -
100T LEU 2.9 15.2 + - - +
101T LEU* 3.6 7.4 - - + +
103T TYR* 1.3 78.2 - - - +
105T LEU* 1.3 55.6 + - + +
107T ARG 3.0 1.9 + - - -
108T GLU 2.7 31.5 + - - -
109T ILE* 2.9 43.0 + - - +
111T PHE* 3.8 26.2 - - + -
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Residues in contact with LEU 105 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101T LEU* 2.8 31.1 + - + +
102T HIS* 3.5 16.4 - - + +
104T CYS* 1.3 77.6 - - + +
106T GLU* 1.3 62.7 + - - +
108T GLU* 3.3 17.3 + - - +
109T ILE 6.1 0.2 - - - +
111T PHE* 6.3 0.4 - - + -
154T ILE* 3.6 32.3 - - + -
158T ALA* 4.4 13.2 - - + -
159T ASN* 5.2 3.3 - - - +
160T SER* 4.3 15.5 + - - +
161T GLN 5.7 0.2 - - - +
162T ILE* 3.7 30.1 - - + -
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Residues in contact with GLU 106 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258O GLN* 5.6 1.8 - - - +
102T HIS* 3.0 19.0 + - - +
103T TYR* 3.8 5.4 - - - +
105T LEU* 1.3 78.3 - - - +
107T ARG* 1.3 80.5 + - + +
108T GLU* 3.4 3.6 - - - +
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Residues in contact with ARG 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63T GLY* 3.5 28.7 + - - -
65T GLU* 3.3 37.6 + - - +
103T TYR* 3.1 64.2 + - - +
104T CYS 3.0 2.4 + - - -
106T GLU* 1.3 101.3 + - + +
108T GLU* 1.3 71.4 + - - +
109T ILE* 3.2 23.8 + - + +
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Residues in contact with GLU 108 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104T CYS 2.7 6.4 + - - -
105T LEU 3.3 10.4 + - - +
106T GLU 4.9 2.2 - - - +
107T ARG* 1.3 81.8 - - - +
109T ILE* 1.3 57.1 + - - +
110T PRO* 3.4 10.2 - - - +
159T ASN* 3.9 31.5 + - + +
160T SER* 3.4 26.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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