Contacts of the helix formed by residues 94 - 110 (chain N) in PDB entry 2I2X
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 PHE 94 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235M ASN 3.6 21.5 - - - -
236M LYS* 3.2 20.9 - - + +
238M LEU 3.6 15.9 - - - -
239M ALA* 3.4 35.9 - - - -
240M HIS* 5.3 2.0 - + - -
417M PHE* 3.4 35.7 - + + -
418M GLU* 6.0 4.0 - - + -
88N TYR* 3.7 6.1 - - - -
91N GLY 4.7 9.2 - - - -
93N ILE* 1.3 81.4 - - - +
95N LEU* 1.3 70.0 + - - +
96N PRO* 3.4 8.5 - - + -
97N ASN* 2.8 30.5 + - - +
98N VAL* 3.5 7.3 + - - +
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Residues in contact with LEU 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177M LEU* 4.3 23.1 - - + -
229M ILE* 5.0 2.0 - - + -
236M LYS 2.9 9.9 + - - -
237M ASN* 3.4 34.8 - - + +
88N TYR* 3.4 13.1 - - + +
94N PHE* 1.3 70.5 - - - +
96N PRO* 1.4 71.0 - - + +
98N VAL* 2.8 21.9 + - + +
99N MET* 3.1 26.2 + - + +
142N ILE* 3.9 47.3 - - + -
146N LEU* 4.3 13.7 - - + -
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Residues in contact with PRO 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M VAL 4.2 1.6 - - - +
177M LEU* 3.0 31.9 - - - +
178M ARG 4.1 0.2 - - - -
179M ASN* 3.2 38.6 - - - +
237M ASN 3.2 20.9 - - - +
238M LEU* 4.2 12.6 - - + +
239M ALA 5.8 0.4 - - - +
94N PHE* 3.6 11.7 - - + -
95N LEU* 1.4 89.3 - - + +
97N ASN* 1.3 51.7 + - - +
99N MET* 3.0 3.5 + - - +
100N MET* 2.8 37.7 + - - +
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Residues in contact with ASN 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179M ASN* 4.0 14.8 + - - +
417M PHE* 3.6 16.5 - - - -
48N PHE* 4.7 4.6 - - + +
93N ILE* 4.1 24.6 - - + +
94N PHE* 2.8 45.6 + - - +
95N LEU 3.1 0.6 - - - -
96N PRO* 1.3 76.9 - - - +
98N VAL* 1.3 57.4 + - - +
100N MET* 3.6 17.2 + - + +
101N SER* 3.0 30.8 + - - -
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Residues in contact with VAL 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81N MET* 4.2 16.2 - - + -
84N VAL* 3.9 18.8 - - + -
85N ILE* 5.6 2.9 - - + -
88N TYR* 3.8 40.2 - - + -
93N ILE* 4.1 3.4 - - + -
94N PHE 3.8 6.3 - - - +
95N LEU* 2.8 15.5 + - + +
97N ASN* 1.3 74.8 - - - +
99N MET* 1.3 56.5 + - - +
101N SER* 2.9 4.2 + - - -
102N ALA* 2.6 35.6 + - + +
145N ALA* 5.5 1.6 - - + +
146N LEU* 4.4 26.2 - - + -
149N ALA* 4.8 5.6 - - + -
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Residues in contact with MET 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177M LEU* 3.3 45.1 - - + +
178M ARG* 3.8 34.3 - - + +
95N LEU* 3.7 26.2 - - + +
96N PRO* 3.3 1.1 - - + +
98N VAL* 1.3 77.9 - - - +
100N MET* 1.3 57.2 + - - +
102N ALA* 3.0 8.9 + - + +
103N ASP* 2.8 37.0 + - - +
141N ASN* 5.1 4.3 - - + +
142N ILE* 5.6 1.8 - - - -
145N ALA* 3.3 35.7 - - + -
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Residues in contact with MET 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178M ARG* 3.3 36.1 - - + +
179M ASN* 4.3 16.4 - - - -
48N PHE 5.7 0.9 - - - +
49N GLU 4.1 20.2 - - - +
50N GLY* 3.4 24.1 - - - +
96N PRO 2.8 18.9 + - - +
97N ASN* 3.7 16.2 - - - +
99N MET* 1.3 71.6 - - - +
101N SER* 1.3 61.2 + - - +
103N ASP* 3.6 6.5 + - - +
104N ALA* 3.2 17.3 + - - +
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Residues in contact with SER 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47N ILE* 2.6 29.1 + - - +
48N PHE 3.2 12.1 + - - -
50N GLY* 4.3 0.4 - - - -
81N MET* 3.6 8.9 - - - +
84N VAL* 3.4 30.6 - - - +
97N ASN 3.0 15.2 + - - -
98N VAL 2.9 9.0 + - - -
100N MET* 1.3 76.3 - - - +
102N ALA* 1.3 57.3 + - - +
104N ALA* 3.6 3.5 + - - +
105N MET* 3.2 26.0 + - - +
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Residues in contact with ALA 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81N MET* 3.5 14.8 - - + +
98N VAL* 2.6 17.4 + - + +
99N MET* 3.0 17.2 + - + +
101N SER* 1.3 71.3 - - - +
103N ASP* 1.3 60.2 + - - +
104N ALA 3.2 1.3 - - - -
105N MET* 3.0 8.8 + - + +
106N LEU* 2.7 42.1 + - + +
145N ALA* 4.9 7.6 - - + +
148N ARG* 6.1 2.2 - - + -
149N ALA* 4.9 9.6 - - + +
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Residues in contact with ASP 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174M TYR* 4.4 6.2 + - - -
178M ARG* 2.7 44.2 + - - +
52N GLU* 4.4 11.5 - - - +
99N MET* 2.8 23.0 + - - +
100N MET* 3.9 6.5 - - - +
102N ALA* 1.3 75.3 - - - +
104N ALA* 1.3 60.1 + - - +
106N LEU* 4.7 5.6 - - - +
107N GLU* 3.3 24.6 + - - +
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Residues in contact with ALA 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47N ILE* 4.6 5.4 - - - +
50N GLY* 3.8 25.1 - - - +
51N GLU 4.0 1.1 - - - +
52N GLU* 4.0 22.1 + - - +
55N VAL* 3.5 34.4 - - + +
100N MET 3.2 16.3 + - - +
101N SER* 3.7 6.3 - - - +
102N ALA 3.2 0.6 - - - -
103N ASP* 1.3 77.4 - - - +
105N MET* 1.3 58.3 + - - +
107N GLU* 4.5 0.7 - - - -
108N GLY 3.7 6.8 + - - -
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Residues in contact with MET 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47N ILE* 4.3 8.7 - - + -
55N VAL* 5.3 0.4 - - - -
77N LEU* 4.0 31.7 - - + +
78N MET* 5.4 7.0 - - - +
81N MET* 4.0 28.7 - - - -
101N SER 3.2 15.5 + - - +
102N ALA* 3.0 11.0 + - + +
104N ALA* 1.3 77.1 - - - +
106N LEU* 1.3 95.3 + - + +
107N GLU 3.1 1.8 - - - -
108N GLY* 2.8 4.1 + - - -
109N ILE* 2.8 42.9 + - + +
148N ARG 3.4 26.7 - - - +
149N ALA* 4.8 2.5 - - - +
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Residues in contact with LEU 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N ALA* 2.7 21.8 + - + +
103N ASP* 5.0 5.8 - - - +
105N MET* 1.3 91.1 - - + +
107N GLU* 1.3 56.5 + - - +
109N ILE* 3.4 22.2 + - + +
110N GLU* 3.3 27.1 + - - +
148N ARG* 3.8 45.8 - - + +
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Residues in contact with GLU 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52N GLU* 3.3 36.1 - - + +
53N ASP* 5.2 2.3 - - - +
56N VAL* 4.2 20.9 - - - +
103N ASP 3.3 19.0 + - - +
104N ALA 4.5 3.1 - - - +
105N MET 3.1 0.4 - - - -
106N LEU* 1.3 76.5 - - - +
108N GLY* 1.3 59.2 + - - +
110N GLU* 3.5 31.5 - - - +
111N TYR* 3.6 11.3 + - - +
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Residues in contact with GLY 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N VAL* 4.3 11.0 - - - -
56N VAL* 5.2 2.7 - - - -
59N LEU* 4.1 4.4 - - - +
77N LEU* 3.6 14.9 - - - +
104N ALA 3.7 9.0 + - - -
105N MET 2.8 11.3 + - - -
107N GLU* 1.3 77.5 - - - +
109N ILE* 1.3 62.6 + - - +
110N GLU 3.2 0.4 - - - -
111N TYR* 3.2 16.9 + - - +
112N CYS* 3.4 18.4 + - - -
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Residues in contact with ILE 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N ILE* 4.1 39.4 - - + +
77N LEU* 3.8 11.0 - - + +
78N MET* 5.6 5.4 - - + -
105N MET* 2.8 40.4 + - + +
106N LEU* 3.4 21.7 + - + +
108N GLY* 1.3 73.2 - - - +
110N GLU* 1.3 56.5 + - - +
112N CYS* 3.9 8.5 + - - +
113N LYS* 3.4 37.1 + - - +
148N ARG 5.6 1.8 - - - +
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Residues in contact with GLU 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106N LEU 3.3 12.7 + - - +
107N GLU* 3.5 31.3 - - - +
109N ILE* 1.3 73.9 - - - +
111N TYR* 1.3 63.2 + - - +
112N CYS 3.2 1.8 - - - -
113N LYS* 3.7 30.9 + - + +
114N GLU* 3.5 21.0 + - - +
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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
------------------------------------------------------------
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