Contacts of the helix formed by residues 93 - 108 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H HIS* 4.9 0.4 + - - -
77H ALA* 3.4 12.8 - - + +
78H CYS* 2.8 46.7 + - - +
89H MET* 2.9 30.5 + - - +
92H ASN* 1.3 82.7 + - - +
94H TYR* 1.3 63.9 + - - +
95H GLN 3.7 0.2 - - - -
97H SER* 2.8 32.8 + - - -
140H PHE* 4.0 7.9 - - - -
143H SER* 3.2 28.2 + - - +
144H LYS* 4.6 7.8 - - + +
147H PHE* 6.0 0.2 - - - -
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Residues in contact with TYR 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H MET 3.7 0.4 + - - -
90H MET* 3.2 37.6 + - + +
93H ASN* 1.3 76.0 - - - +
95H GLN* 1.3 73.9 + - - +
97H SER* 3.2 6.2 + - - -
98H LYS* 2.9 40.2 + - + +
143H SER* 4.1 9.9 - - - +
146H LEU* 3.5 45.7 - - + +
147H PHE* 3.6 27.0 - + + -
150H TYR* 3.7 16.0 - - + +
48I ALA 4.3 0.9 + - - -
49I ASP* 2.4 38.5 + - - -
50I TYR* 3.6 15.7 + + - -
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Residues in contact with GLN 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H MET 2.8 15.4 + - - +
91H ASP* 3.3 27.8 - - - +
94H TYR* 1.3 77.0 - - - +
96H TYR* 1.3 63.2 - - - +
98H LYS* 3.0 41.9 + - - +
99H GLU* 3.0 47.9 + - - +
50I TYR 4.1 10.4 - - - +
51I MET* 5.5 5.8 - - - +
55I ASP* 5.6 3.6 - - - +
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Residues in contact with TYR 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H THR* 5.4 0.9 - - + -
30H VAL* 4.1 0.2 - - - +
53H LYS* 2.7 41.8 + - + +
54H GLU* 5.5 1.1 - - - -
56H PHE* 3.5 18.4 - + - -
57H LEU* 3.6 34.2 + - + -
74H HIS* 3.9 15.3 - + - -
91H ASP 2.9 13.5 + - - +
92H ASN* 3.1 26.2 - - - +
93H ASN 4.0 0.2 - - - +
94H TYR 3.3 0.2 - - - -
95H GLN* 1.3 73.8 - - - +
97H SER* 1.3 65.3 + - - +
99H GLU* 3.0 17.6 + - - +
100H LEU* 3.0 31.7 + - + +
400H NAP 3.4 37.1 + + - -
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Residues in contact with SER 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H HIS* 2.8 33.1 + - - -
76H GLY 5.2 0.2 + - - -
93H ASN* 2.8 22.5 + - - -
94H TYR 3.5 3.8 - - - -
96H TYR* 1.3 79.3 - - - +
98H LYS* 1.3 63.5 + - - +
99H GLU 3.2 0.2 + - - -
100H LEU* 3.3 3.7 + - - +
101H LEU* 2.9 23.7 + - - +
111H PHE* 4.1 0.9 - - - -
113H TYR* 5.9 0.3 - - - -
144H LYS* 5.6 3.6 + - - -
147H PHE* 3.6 33.0 - - - +
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Residues in contact with LYS 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H TYR* 2.9 30.5 + - + +
95H GLN* 3.0 44.8 + - - +
97H SER* 1.3 76.2 - - - +
99H GLU* 1.3 64.4 + - - +
101H LEU* 3.2 3.2 + - - +
102H HIS* 3.0 36.4 + - + +
147H PHE* 3.5 12.3 - - + -
150H TYR* 3.6 45.4 + - + +
49I ASP* 2.9 31.2 + - - +
50I TYR 4.2 2.2 + - - -
51I MET* 5.2 4.8 - - - +
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Residues in contact with GLU 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H LEU* 4.0 14.4 - - + -
60H ILE* 3.9 8.8 - - + +
61H MET* 3.4 44.3 - - + +
95H GLN* 3.0 38.6 + - - +
96H TYR 3.0 10.1 + - - +
98H LYS* 1.3 79.4 - - - +
100H LEU* 1.3 62.8 + - - +
102H HIS* 3.4 8.2 + - - +
103H TYR* 3.2 21.5 + - - +
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Residues in contact with LEU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H THR* 4.1 14.6 - - + -
56H PHE* 3.7 24.2 - - + -
57H LEU* 5.2 2.2 - - + -
60H ILE* 3.9 17.9 - - + -
72H ILE* 4.5 12.1 - - + -
74H HIS* 3.3 46.0 - - + +
96H TYR* 3.0 24.7 + - + +
97H SER 3.6 7.4 - - - +
99H GLU* 1.3 74.4 - - - +
101H LEU* 1.3 66.8 + - - +
103H TYR* 3.1 7.6 + - - +
104H CYS* 2.9 26.2 + - - -
111H PHE* 3.7 13.5 - - + -
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Residues in contact with LEU 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H SER 2.9 17.7 + - - +
98H LYS 3.5 3.8 - - - +
100H LEU* 1.3 76.4 - - - +
102H HIS* 1.3 59.4 + - + +
104H CYS* 3.3 1.0 + - - +
105H LEU* 2.8 42.4 + - + +
111H PHE* 3.8 31.2 - - + -
147H PHE* 4.0 20.9 - - + -
150H TYR* 4.0 28.7 - - + -
151H VAL* 4.3 9.0 - - + -
154H ILE* 4.3 13.9 - - + -
162H ILE* 3.8 28.9 - - + -
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Residues in contact with HIS 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H LYS* 3.0 34.7 + - + +
99H GLU* 3.9 8.5 - - - +
101H LEU* 1.3 77.7 - - + +
103H TYR* 1.3 64.0 + - - +
105H LEU* 3.3 13.6 + - + +
106H GLU* 3.0 29.9 + - - +
150H TYR* 2.6 38.5 + + - -
154H ILE* 4.5 14.4 - - + -
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Residues in contact with TYR 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE* 6.0 0.4 - - + -
60H ILE* 3.5 57.2 - - + -
63H GLY* 4.3 0.9 - - - -
64H GLU 2.6 29.0 + - - -
65H GLU* 3.8 5.0 + - - -
66H PHE* 3.3 17.7 + + - -
69H VAL* 5.6 2.6 - - + +
72H ILE* 4.7 7.4 - - + -
99H GLU 3.2 13.3 + - - +
100H LEU* 3.1 8.2 + - - +
102H HIS* 1.3 77.7 - - - +
104H CYS* 1.3 72.4 + - - +
106H GLU* 4.8 1.3 - - - -
107H ARG* 3.1 79.7 + - - +
109H ILE* 4.1 13.2 - - + +
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Residues in contact with CYS 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H ILE* 3.4 36.6 - - - -
100H LEU 2.9 14.8 + - - +
101H LEU* 3.6 7.6 - - + +
103H TYR* 1.3 78.9 - - - +
105H LEU* 1.3 56.2 + - + +
107H ARG 3.0 1.9 + - - -
108H GLU 2.7 31.5 + - - -
109H ILE* 2.9 41.3 + - - +
111H PHE* 3.8 27.4 - - + -
160H SER* 4.9 0.2 - - - -
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Residues in contact with LEU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H LEU* 2.8 32.3 + - + +
102H HIS* 3.5 16.4 - - - +
104H CYS* 1.3 75.7 - - + +
106H GLU* 1.3 63.4 + - - +
108H GLU* 3.3 17.0 + - - +
109H ILE 6.1 0.2 - - - +
111H PHE* 6.3 0.2 - - + -
154H ILE* 3.5 32.5 - - + -
158H ALA* 4.3 12.8 - - + -
159H ASN* 5.3 2.8 - - - +
160H SER* 4.3 15.2 + - - +
161H GLN 5.7 0.2 - - - +
162H ILE* 3.7 28.5 - - + -
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Residues in contact with GLU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H HIS* 3.0 19.6 + - - +
103H TYR* 3.8 5.5 - - - +
105H LEU* 1.3 77.9 - - - +
107H ARG* 1.3 79.9 + - + +
108H GLU* 3.4 3.6 - - - +
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Residues in contact with ARG 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H GLY* 3.5 29.1 + - - -
65H GLU* 3.3 37.8 + - - +
103H TYR* 3.1 63.9 + - - +
104H CYS 3.0 2.0 + - - -
106H GLU* 1.3 103.1 + - + +
108H GLU* 1.3 71.2 + - - +
109H ILE* 3.2 23.6 + - + +
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Residues in contact with GLU 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H CYS 2.7 5.2 + - - -
105H LEU 3.3 10.4 + - - +
106H GLU 4.9 3.1 - - - +
107H ARG* 1.3 82.0 - - - +
109H ILE* 1.3 57.6 + - - +
110H PRO* 3.4 10.7 - - - +
159H ASN* 3.9 31.3 + - + +
160H SER* 3.4 27.8 - - - +
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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