Contacts of the helix formed by residues 94 - 113 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E ASN* 6.1 0.2 - - - +
235E ASN 3.4 19.1 - - - -
236E LYS* 3.2 32.1 - - + -
237E ASN 4.0 0.2 - - - -
238E LEU 3.5 30.3 - - - -
239E ALA* 3.6 16.2 - - - -
240E HIS* 5.2 3.4 - + - -
417E PHE* 3.4 36.8 - + + -
418E GLU* 6.1 3.1 - - + -
88F TYR* 3.8 5.4 - - - -
91F GLY 4.6 8.7 - - - -
93F ILE* 1.3 81.3 - - - +
95F LEU* 1.3 64.6 + - - +
96F PRO* 3.4 8.1 - - + -
97F ASN* 2.9 34.4 - - - +
98F VAL* 3.3 10.9 + - - +
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Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E LEU* 4.2 24.5 - - + +
229E ILE* 4.9 3.1 - - + -
236E LYS 3.0 6.1 + - - -
237E ASN* 3.2 42.2 - - + +
88F TYR* 3.7 13.4 - - + +
94F PHE* 1.3 76.5 - - - +
96F PRO* 1.4 59.0 - - + +
98F VAL* 2.8 28.8 + - + +
99F MET* 2.9 26.4 + - + +
142F ILE* 3.7 47.1 - - + -
145F ALA* 6.1 0.9 - - + -
146F LEU* 5.4 2.2 - - + -
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Residues in contact with PRO 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E VAL 4.4 0.9 - - - +
177E LEU* 3.2 28.0 - - - +
178E ARG 4.1 0.4 - - - -
179E ASN* 3.3 46.0 - - - +
237E ASN 3.3 14.4 - - - +
238E LEU* 4.2 11.7 - - + -
239E ALA 5.7 0.4 - - - +
94F PHE* 3.6 12.8 - - + -
95F LEU* 1.4 95.0 - - + +
97F ASN* 1.3 54.6 + - - +
99F MET* 3.9 0.7 - - + +
100F MET* 2.9 36.5 + - - +
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Residues in contact with ASN 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E ASN* 5.0 8.5 + - - +
417E PHE* 3.3 23.2 - - - -
48F PHE 4.6 5.3 - - - +
84F VAL* 4.4 1.6 - - - +
93F ILE* 3.9 25.6 - - + +
94F PHE* 2.9 38.0 + - - +
96F PRO* 1.3 77.0 - - - +
98F VAL* 1.3 56.3 + - - +
100F MET* 4.1 8.5 - - - +
101F SER* 3.0 29.5 + - - -
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Residues in contact with VAL 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F MET* 3.6 10.3 - - + +
84F VAL* 4.0 15.9 - - + -
85F ILE* 5.3 6.3 - - + -
88F TYR* 3.6 36.6 - - + -
93F ILE* 3.9 8.7 - - + -
94F PHE 3.3 15.7 - - - +
95F LEU* 2.8 15.1 + - + +
97F ASN* 1.3 73.9 - - - +
99F MET* 1.3 62.1 + - + +
101F SER 3.3 0.2 + - - -
102F ALA* 2.8 29.4 + - + +
145F ALA* 5.7 6.5 - - + -
146F LEU* 4.9 18.2 - - + -
149F ALA* 5.3 6.7 - - + -
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Residues in contact with MET 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E LEU* 3.3 42.6 - - + +
178E ARG* 3.8 32.5 - - + +
95F LEU* 2.9 32.5 + - + +
96F PRO 3.9 0.4 - - - +
98F VAL* 1.3 74.1 - - - +
100F MET* 1.3 58.5 + - - +
102F ALA* 3.2 6.6 + - + +
103F ASP* 2.9 39.3 + - - +
141F ASN* 4.6 9.9 - - + +
142F ILE* 5.2 3.8 - - - -
145F ALA* 3.7 30.1 - - + -
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Residues in contact with MET 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E ARG* 3.3 34.3 - - + +
179E ASN* 4.8 8.1 - - - -
49F GLU 4.4 15.5 - - - +
50F GLY* 3.4 26.1 - - - +
96F PRO 2.9 21.7 + - - +
97F ASN* 4.2 8.3 - - - +
99F MET* 1.3 75.9 - - - +
101F SER* 1.3 57.6 + - - +
103F ASP* 3.6 8.2 + - - +
104F ALA* 3.2 21.1 + - - +
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Residues in contact with SER 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ILE* 2.6 31.9 + - - +
48F PHE 3.3 13.0 + - - -
50F GLY* 4.1 1.6 + - - -
81F MET* 3.7 15.9 - - - +
84F VAL* 3.5 16.5 - - - +
97F ASN 3.0 21.3 + - - -
98F VAL 3.6 4.0 - - - -
99F MET 3.2 0.4 - - - -
100F MET* 1.3 77.4 - - - +
102F ALA* 1.3 59.3 + - - +
104F ALA* 3.4 3.3 + - - +
105F MET* 3.1 26.0 + - - +
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Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F MET* 3.4 18.6 - - + +
98F VAL* 2.8 19.3 + - + +
99F MET* 3.7 9.0 - - + +
101F SER* 1.3 73.1 - - - +
103F ASP* 1.3 58.8 + - - +
105F MET* 3.0 13.0 + - + +
106F LEU* 2.7 44.1 + - + +
145F ALA* 5.0 14.6 - - + +
148F ARG* 6.1 1.3 - - + -
149F ALA* 5.0 6.5 - - + +
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Residues in contact with ASP 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174E TYR* 4.8 2.9 + - - -
178E ARG* 3.0 39.4 + - - +
52F GLU* 5.2 0.8 - - - +
99F MET* 2.9 21.5 + - - +
100F MET* 3.7 8.4 - - - +
102F ALA* 1.3 76.3 - - - +
104F ALA* 1.3 57.1 + - - +
106F LEU* 3.7 12.5 + - - +
107F GLU* 3.2 29.1 + - - +
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Residues in contact with ALA 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ILE* 4.7 4.0 - - - +
50F GLY* 3.8 24.9 - - - +
51F GLU 4.0 3.6 - - - +
52F GLU* 4.0 17.1 - - + +
55F VAL* 3.5 37.9 - - + +
100F MET 3.2 15.2 + - - +
101F SER 3.7 5.6 - - - +
102F ALA 3.2 0.2 - - - -
103F ASP* 1.3 78.4 - - - +
105F MET* 1.3 59.4 + - - +
107F GLU* 4.2 2.0 - - - +
108F GLY 3.5 5.8 + - - -
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Residues in contact with MET 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ILE* 4.2 10.8 - - + -
77F LEU* 4.1 23.9 - - + +
78F MET* 4.4 13.5 - - - +
81F MET* 3.9 28.9 - - - -
101F SER 3.1 12.5 + - - +
102F ALA* 3.0 16.7 + - + +
104F ALA* 1.3 77.5 - - - +
106F LEU* 1.3 75.2 + - + +
107F GLU 3.1 1.3 - - - -
108F GLY* 3.0 2.6 + - - +
109F ILE* 2.7 52.2 + - + +
148F ARG* 3.8 30.7 - - + +
149F ALA* 4.3 3.6 - - - -
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ALA* 2.7 28.4 + - + +
103F ASP* 4.2 12.8 - - - +
105F MET* 1.3 83.1 - - + +
107F GLU* 1.3 59.1 + - - +
109F ILE* 3.7 12.8 + - + +
110F GLU* 3.4 23.9 + - - +
148F ARG* 3.8 44.2 - - + +
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Residues in contact with GLU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F GLU* 3.8 33.0 - - + +
56F VAL* 4.4 15.6 - - - +
103F ASP 3.2 18.5 + - - +
104F ALA 4.6 2.9 - - - +
105F MET 3.1 0.6 - - - -
106F LEU* 1.3 75.7 - - - +
108F GLY* 1.3 61.0 + - - +
110F GLU* 4.2 17.1 - - - +
111F TYR* 3.7 18.7 + - - +
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Residues in contact with GLY 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F VAL* 4.0 17.2 - - - +
56F VAL* 4.9 3.8 - - - -
59F LEU* 3.3 12.1 - - - +
77F LEU* 3.5 7.4 - - - +
104F ALA 3.5 11.2 + - - -
105F MET 3.0 9.0 + - - -
107F GLU* 1.3 79.2 - - - +
109F ILE* 1.3 61.4 + - - +
111F TYR* 3.9 4.2 + - - +
112F CYS* 3.3 24.1 + - - -
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Residues in contact with ILE 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F ILE* 4.1 31.9 - - + +
77F LEU* 3.6 17.0 - - + -
78F MET* 5.8 3.4 - - - -
105F MET* 2.7 43.2 + - + +
106F LEU* 3.9 13.2 - - + +
108F GLY* 1.3 76.3 - - - +
110F GLU* 1.3 60.0 + - + +
111F TYR 3.1 1.1 - - - -
112F CYS* 3.0 28.3 + - - +
113F LYS* 3.4 18.2 + - + +
120F PRO* 5.6 5.4 - - + -
148F ARG 5.9 1.1 - - - +
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Residues in contact with GLU 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU 3.4 16.4 + - - +
107F GLU* 4.2 18.0 - - + +
109F ILE* 1.3 80.8 - - + +
111F TYR* 1.3 60.5 + - - +
113F LYS* 3.5 29.7 - - + +
114F GLU* 3.9 14.6 + - - +
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Residues in contact with TYR 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F VAL* 4.0 42.2 - - + -
59F LEU* 4.3 22.7 - - + -
60F GLN* 3.4 26.1 + - + +
63F ILE* 5.6 4.9 - - + -
107F GLU 3.7 14.6 + - - +
108F GLY 3.9 6.1 - - - +
109F ILE 3.1 0.4 - - - -
110F GLU* 1.3 79.2 - - + +
112F CYS* 1.3 67.7 + - - +
113F LYS 3.2 0.7 - - - -
114F GLU* 3.3 36.1 + - + +
115F ASN* 3.6 28.4 + - - -
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Residues in contact with CYS 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F LEU* 3.9 23.3 - - - -
63F ILE* 5.9 4.5 - - - -
69F PRO* 3.6 28.3 - - - +
70F ILE* 4.5 4.0 - - - +
72F LEU* 5.1 2.5 - - - -
73F ILE* 4.2 23.3 - - + -
77F LEU* 4.7 1.6 - - - -
108F GLY 3.3 18.4 - - - -
109F ILE 3.0 9.9 + - - +
111F TYR* 1.3 76.5 - - - +
113F LYS* 1.3 58.5 + - - +
114F GLU 3.3 0.2 - - - -
115F ASN* 3.4 10.0 + - - +
116F SER* 3.2 27.3 + - - -
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Residues in contact with LYS 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ILE* 5.5 1.1 - - + +
109F ILE* 3.4 18.1 + - + +
110F GLU* 3.5 25.5 - - + +
111F TYR 3.2 0.2 - - - -
112F CYS* 1.3 76.1 - - - +
114F GLU* 1.3 62.6 + - + +
116F SER* 2.9 25.5 + - - +
117F GLY 4.5 0.7 + - - -
120F PRO* 4.0 33.6 - - + +
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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