Contacts of the helix formed by residues 93 - 108 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L ALA* 3.4 11.7 - - + +
78L CYS* 2.8 46.3 + - - +
89L MET* 2.9 27.4 + - - +
92L ASN* 1.3 83.8 + - - +
94L TYR* 1.3 63.4 + - - +
97L SER* 2.8 33.4 + - - -
140L PHE* 4.0 8.1 - - - -
143L SER* 3.2 29.2 + - - +
144L LYS* 4.6 7.8 - - + +
147L PHE* 6.0 0.4 - - - -
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Residues in contact with TYR 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89L MET 3.7 0.4 + - - -
90L MET* 3.2 36.7 + - + +
93L ASN* 1.3 76.2 - - - +
95L GLN* 1.3 73.4 + - - +
97L SER* 3.2 6.1 + - - -
98L LYS* 2.9 40.5 + - + +
143L SER* 4.1 9.4 - - - +
146L LEU* 3.5 44.1 + - + +
147L PHE* 3.6 28.6 - + + -
150L TYR* 3.7 16.1 - - + +
48M ALA 4.3 0.7 + - - -
49M ASP* 2.3 42.1 + - - -
50M TYR* 3.6 14.1 - + - -
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Residues in contact with GLN 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90L MET 2.8 15.1 + - - +
91L ASP* 3.3 26.2 - - - +
94L TYR* 1.3 77.3 - - + +
96L TYR* 1.3 64.7 + - - +
98L LYS* 3.0 43.2 + - - +
99L GLU* 3.0 47.3 + - - +
50M TYR 4.1 10.0 - - - +
51M MET* 5.4 5.7 - - - +
55M ASP* 5.6 3.8 - - - +
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Residues in contact with TYR 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5L THR* 5.4 0.9 - - + -
30L VAL* 4.1 0.3 - - - +
53L LYS* 2.7 41.3 + - + +
54L GLU* 5.4 1.3 - - - -
56L PHE* 3.5 18.0 - + - -
57L LEU* 3.6 33.9 + - + -
74L HIS* 3.9 16.8 - + - +
91L ASP 2.9 12.4 + - - +
92L ASN* 3.0 25.4 - - - +
94L TYR 3.3 0.2 - - - -
95L GLN* 1.3 75.3 - - - +
97L SER* 1.3 63.9 + - - +
99L GLU* 3.0 17.4 + - - +
100L LEU* 3.0 33.1 + - + +
400L NAP 3.4 36.6 + + - -
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Residues in contact with SER 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74L HIS* 2.8 32.8 + - - -
76L GLY 5.2 0.2 + - - -
93L ASN* 2.8 22.1 + - - -
94L TYR 3.5 2.9 - - - -
96L TYR* 1.3 80.3 - - - +
98L LYS* 1.3 62.5 + - - +
100L LEU* 3.3 2.9 + - - +
101L LEU* 2.9 25.5 + - - +
111L PHE* 4.1 1.0 - - - -
113L TYR* 5.9 0.2 - - - -
144L LYS* 5.6 3.3 + - - -
147L PHE* 3.6 33.9 - - - -
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Residues in contact with LYS 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94L TYR* 2.9 30.1 + - + +
95L GLN* 3.0 46.0 + - - +
97L SER* 1.3 76.6 - - - +
99L GLU* 1.3 64.8 + - - +
101L LEU* 3.2 3.1 + - - +
102L HIS* 3.0 37.6 + - + +
147L PHE* 3.5 11.9 - - + -
150L TYR* 3.6 45.9 + - + +
49M ASP* 3.0 31.6 + - - +
50M TYR 4.2 2.0 + - - -
51M MET* 5.1 5.3 - - - +
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Residues in contact with GLU 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L LEU* 4.0 15.5 - - + -
60L ILE* 3.9 8.6 - - + +
61L MET* 3.4 43.4 - - + +
95L GLN* 3.0 38.3 + - - +
96L TYR 3.2 9.4 - - - +
98L LYS* 1.3 78.7 - - - +
100L LEU* 1.3 61.4 + - - +
102L HIS* 3.4 8.4 + - - +
103L TYR* 3.2 21.3 + - - +
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Residues in contact with LEU 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5L THR* 4.1 13.9 - - + -
56L PHE* 3.7 24.7 - - + -
57L LEU* 5.2 2.2 - - + -
60L ILE* 3.9 18.6 - - + -
72L ILE* 4.5 12.8 - - + -
74L HIS* 3.3 46.7 - - + +
96L TYR* 3.0 23.5 + - + +
97L SER 3.6 7.6 - - - +
99L GLU* 1.3 74.9 - - - +
101L LEU* 1.3 67.4 + - - +
103L TYR* 3.1 7.2 + - - +
104L CYS* 2.9 26.5 + - - -
111L PHE* 3.7 13.5 - - + -
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Residues in contact with LEU 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97L SER 2.9 16.6 + - - +
98L LYS 3.5 4.3 - - - +
100L LEU* 1.3 77.9 - - - +
102L HIS* 1.3 59.4 + - + +
104L CYS* 3.3 1.6 + - - +
105L LEU* 2.8 41.6 + - + +
111L PHE* 3.8 30.5 - - + -
147L PHE* 4.0 20.6 - - + -
150L TYR* 4.0 28.7 - - + -
151L VAL* 4.3 9.2 - - + -
154L ILE* 4.3 13.9 - - + -
162L ILE* 3.8 29.8 - - + -
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Residues in contact with HIS 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L LYS* 3.0 34.8 + - + +
99L GLU* 3.9 8.3 - - - +
100L LEU 3.2 0.2 - - - -
101L LEU* 1.3 78.0 - - + +
103L TYR* 1.3 64.7 + - - +
105L LEU* 3.3 13.8 + - + +
106L GLU* 3.0 29.9 + - - +
150L TYR* 2.6 37.8 + + - -
154L ILE* 4.5 14.6 - - + -
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Residues in contact with TYR 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L ILE* 3.5 59.2 - - + +
63L GLY* 4.3 0.7 - - - -
64L GLU 2.6 27.4 + - - -
65L GLU* 3.8 5.4 + - - -
66L PHE* 3.3 18.3 + + - -
69L VAL* 5.6 3.1 - - + +
72L ILE* 4.7 7.2 - - + -
99L GLU 3.2 12.9 + - - +
100L LEU 3.1 9.1 + - - +
102L HIS* 1.3 76.8 - - - +
104L CYS* 1.3 71.6 + - - +
106L GLU* 3.6 1.5 + - - -
107L ARG* 3.1 77.6 + - - +
109L ILE* 4.1 13.2 - - + +
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Residues in contact with CYS 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L ILE* 3.4 36.8 - - - -
100L LEU 2.9 14.8 + - - +
101L LEU* 3.6 7.0 - - + +
103L TYR* 1.3 78.3 - - - +
105L LEU* 1.3 56.2 + - + +
107L ARG 3.0 1.7 + - - -
108L GLU 2.7 31.7 + - - -
109L ILE* 2.9 41.1 + - - +
111L PHE* 3.8 26.2 - - + -
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Residues in contact with LEU 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L LEU* 2.8 31.9 + - + +
102L HIS* 3.3 15.9 + - + +
104L CYS* 1.3 76.7 - - + +
106L GLU* 1.3 62.7 + - - +
108L GLU* 3.3 17.3 + - - +
109L ILE 6.1 0.2 - - - +
111L PHE* 6.3 0.4 - - + -
154L ILE* 3.5 32.5 - - + -
158L ALA* 4.3 13.7 - - + -
159L ASN* 5.3 2.2 - - - +
160L SER* 4.3 15.6 + - - +
161L GLN 5.7 0.2 - - - +
162L ILE* 3.7 29.8 - - + -
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Residues in contact with GLU 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102L HIS* 3.0 19.5 + - - +
103L TYR* 3.8 5.7 - - - +
104L CYS 3.1 0.2 - - - -
105L LEU* 1.3 78.3 - - - +
107L ARG* 1.3 79.9 + - + +
108L GLU* 3.4 3.8 - - - +
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Residues in contact with ARG 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L GLY* 3.5 28.3 + - - -
65L GLU* 3.3 37.4 + - - +
103L TYR* 3.1 63.8 + - - +
104L CYS 3.0 1.8 + - - -
106L GLU* 1.3 102.8 + - + +
108L GLU* 1.3 71.1 - - - +
109L ILE* 3.2 23.5 + - + +
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Residues in contact with GLU 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L CYS 2.7 5.0 + - - -
105L LEU 3.3 9.9 + - - +
106L GLU 4.9 3.1 - - - +
107L ARG* 1.3 82.1 - - - +
109L ILE* 1.3 58.1 + - - +
110L PRO* 3.4 10.2 - - - +
159L ASN* 3.9 31.4 + - + +
160L SER* 3.4 29.2 - - - +
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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