Contacts of the helix formed by residues 94 - 113 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235K ASN 3.7 15.9 - - - -
236K LYS* 3.1 36.6 - - + +
238K LEU 3.7 6.7 - - - -
239K ALA* 3.6 32.5 - - - -
240K HIS* 5.3 2.0 - + - -
417K PHE* 3.5 38.6 - + + -
418K GLU* 6.0 4.0 - - + -
88L TYR* 3.7 5.6 - - - -
91L GLY 4.3 11.2 - - - -
93L ILE* 1.3 83.2 - - - +
95L LEU* 1.3 66.4 + - - +
96L PRO* 3.4 11.2 - - + -
97L ASN* 3.2 28.9 + - - +
98L VAL* 3.4 7.1 + - - +
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Residues in contact with LEU 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177K LEU* 4.4 21.5 - - + -
229K ILE* 4.8 3.4 - - + -
236K LYS 3.1 5.9 + - - -
237K ASN* 3.4 36.1 - - + +
88L TYR* 3.4 14.2 - - + +
94L PHE* 1.3 74.6 - - - +
96L PRO* 1.4 70.3 - - + +
98L VAL* 2.9 15.0 + - + +
99L MET* 2.9 39.9 + - + +
142L ILE* 3.6 46.4 - - + -
146L LEU* 4.8 4.5 - - + -
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Residues in contact with PRO 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176K VAL 4.2 5.2 - - - +
177K LEU* 3.2 27.5 - - - +
178K ARG* 4.1 0.9 - - - -
179K ASN* 3.3 39.5 - - - +
237K ASN 3.2 24.7 - - - +
238K LEU* 4.1 13.5 - - + -
239K ALA 5.6 0.2 - - - +
94L PHE* 3.6 9.6 - - + -
95L LEU* 1.4 86.5 - - + +
97L ASN* 1.3 62.7 + - - +
99L MET* 3.2 1.0 + - - +
100L MET* 2.9 29.9 + - - +
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Residues in contact with ASN 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179K ASN* 4.4 14.0 + - - +
417K PHE* 3.3 23.0 - - - -
48L PHE* 5.0 4.6 - - + +
93L ILE* 3.9 25.5 - - + +
94L PHE* 3.2 33.9 + - - +
95L LEU 3.2 0.2 + - - -
96L PRO* 1.3 76.0 - - - +
98L VAL* 1.3 57.0 + - - +
100L MET* 3.4 13.2 + - - +
101L SER* 3.0 32.0 + - - -
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Residues in contact with VAL 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81L MET* 3.9 16.1 - - + +
84L VAL* 3.9 18.8 - - + +
85L ILE* 5.6 3.1 - - + -
88L TYR* 3.6 39.9 - - + -
93L ILE* 4.0 3.6 - - + +
94L PHE 3.4 8.5 + - - +
95L LEU* 2.9 13.6 + - + +
97L ASN* 1.3 72.9 - - - +
99L MET* 1.3 56.1 + - - +
101L SER* 3.1 4.9 + - - -
102L ALA* 2.8 34.8 + - + +
145L ALA* 5.3 2.2 - - + +
146L LEU* 4.3 26.2 - - + -
149L ALA* 5.7 2.2 - - + -
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Residues in contact with MET 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177K LEU* 3.3 48.0 - - + +
178K ARG* 4.0 26.2 - - + +
95L LEU* 2.9 38.2 + - + +
96L PRO 3.7 0.7 - - - +
98L VAL* 1.3 72.7 - - - +
100L MET* 1.3 57.2 + - - +
102L ALA* 3.2 6.6 + - + +
103L ASP* 3.0 36.7 + - - +
141L ASN* 4.5 11.2 - - + +
142L ILE* 5.1 2.9 - - - -
145L ALA* 3.6 32.5 - - + -
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Residues in contact with MET 100 (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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178K ARG* 3.6 35.4 - - + +
179K ASN* 4.6 11.0 - - - -
49L GLU 4.0 20.2 - - - +
50L GLY* 3.7 18.3 - - - +
52L GLU* 5.1 0.5 - - - +
96L PRO 2.9 21.0 + - - +
97L ASN* 3.5 11.7 - - - +
99L MET* 1.3 75.4 - - - +
101L SER* 1.3 58.1 + - - +
103L ASP* 3.3 11.2 + - - +
104L ALA* 3.1 25.6 + - - +
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Residues in contact with SER 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L ILE* 2.6 30.7 + - - +
48L PHE 3.4 8.5 + - - -
50L GLY* 4.1 2.6 + - - -
81L MET* 3.8 8.4 - - - +
84L VAL* 3.4 30.8 - - - +
97L ASN 3.0 15.4 + - - -
98L VAL 3.1 8.3 + - - -
100L MET* 1.3 74.3 - - - +
102L ALA* 1.3 58.7 + - - +
104L ALA* 3.4 3.3 + - - +
105L MET* 3.0 27.9 + - - +
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Residues in contact with ALA 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81L MET* 4.0 18.1 - - + +
98L VAL* 2.8 16.7 + - + +
99L MET* 3.2 16.8 + - + +
101L SER* 1.3 72.9 - - - +
103L ASP* 1.3 63.1 + - - +
105L MET* 3.9 7.6 - - + +
106L LEU* 3.0 33.5 + - + +
145L ALA* 4.8 20.0 - - + +
148L ARG* 6.5 0.7 - - + -
149L ALA* 5.9 0.2 - - + -
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Residues in contact with ASP 103 (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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174K TYR* 4.8 4.2 + - - -
178K ARG* 2.8 42.8 + - - +
52L GLU* 5.1 8.1 - - - +
99L MET* 3.0 19.9 + - - +
100L MET* 3.3 9.4 + - - +
102L ALA* 1.3 77.7 - - - +
104L ALA* 1.3 63.9 + - - +
106L LEU* 3.6 10.5 + - - +
107L GLU* 3.3 27.7 + - - +
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Residues in contact with ALA 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L ILE* 4.5 5.4 - - - -
50L GLY* 3.9 24.5 - - - +
51L GLU 4.1 0.2 - - - +
52L GLU* 4.1 15.5 + - - +
55L VAL* 3.6 35.7 - - + +
100L MET 3.1 13.2 + - - +
101L SER* 3.6 9.4 - - - +
103L ASP* 1.3 77.6 - - - +
105L MET* 1.3 58.2 + - - +
107L GLU* 3.8 2.8 + - - +
108L GLY 3.4 14.7 + - - -
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Residues in contact with MET 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L ILE* 4.5 10.7 - - + +
77L LEU* 4.1 31.2 - - + +
78L MET* 5.0 8.5 - - - +
81L MET* 4.1 28.7 - - + +
101L SER 3.0 17.3 + - - +
102L ALA* 3.5 10.1 + - + +
103L ASP 3.3 0.2 - - - -
104L ALA* 1.3 76.8 - - - +
106L LEU* 1.3 77.8 + - + +
108L GLY* 3.4 1.3 + - - +
109L ILE* 3.0 51.4 + - + +
148L ARG* 4.7 26.0 - - + +
149L ALA* 4.8 2.2 - - - +
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Residues in contact with LEU 106 (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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102L ALA* 3.0 21.2 + - + +
103L ASP* 3.6 10.1 + - - +
105L MET* 1.3 92.1 - - + +
107L GLU* 1.3 58.2 + - - +
109L ILE* 3.2 14.9 + - + +
110L GLU* 3.0 30.2 + - - +
148L ARG* 4.2 35.4 - - + +
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Residues in contact with GLU 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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52L GLU* 3.0 38.0 - - + +
53L ASP* 5.2 4.0 - - - +
56L VAL* 4.6 15.3 - - + +
103L ASP 3.3 14.4 + - - +
104L ALA 4.0 4.3 - - - +
105L MET 3.3 0.4 - - - -
106L LEU* 1.3 74.8 - - - +
108L GLY* 1.3 63.6 + - - +
110L GLU* 3.5 21.5 - - + +
111L TYR* 3.3 22.0 + - - +
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Residues in contact with GLY 108 (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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55L VAL* 4.1 15.0 - - - +
56L VAL* 5.4 1.6 - - - -
59L LEU* 3.8 18.0 - - - +
77L LEU* 3.6 9.0 - - - -
104L ALA 3.4 8.3 + - - -
105L MET 3.4 3.3 + - - -
106L LEU 3.3 0.2 - - - -
107L GLU* 1.3 78.6 - - - +
109L ILE* 1.3 60.9 + - - +
111L TYR* 3.3 6.1 - - - +
112L CYS* 3.2 26.9 + - - -
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Residues in contact with ILE 109 (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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73L ILE* 3.8 27.7 - - + +
77L LEU* 3.7 17.7 - - + -
78L MET* 5.7 3.8 - - + -
105L MET* 3.0 48.0 + - + +
106L LEU* 3.2 14.5 + - + +
108L GLY* 1.3 78.1 - - - +
110L GLU* 1.3 62.5 + - + +
112L CYS* 3.4 9.1 + - - +
113L LYS* 3.3 33.5 + - - +
120L PRO* 5.7 4.0 - - + +
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Residues in contact with GLU 110 (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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106L LEU 3.0 15.3 + - - +
107L GLU* 3.5 27.3 - - - +
109L ILE* 1.3 75.8 - - + +
111L TYR* 1.3 67.7 + - - +
112L CYS 3.2 0.7 - - - -
113L LYS* 3.1 27.1 + - + +
114L GLU* 3.4 14.3 + - - +
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Residues in contact with TYR 111 (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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56L VAL* 3.7 33.4 - - + -
59L LEU* 4.1 21.8 - - + -
60L GLN* 2.7 43.6 + - + +
63L ILE* 4.9 8.3 - - + -
107L GLU 3.3 16.4 + - - +
108L GLY* 3.3 13.2 - - - +
109L ILE 3.3 0.2 - - - -
110L GLU* 1.3 79.1 - - - +
112L CYS* 1.3 56.2 + - - +
114L GLU* 3.2 36.5 - - - +
115L ASN* 3.2 37.1 + - - -
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Residues in contact with CYS 112 (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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59L LEU* 4.3 20.0 - - - -
63L ILE* 6.4 1.6 - - - -
69L PRO 3.6 26.1 - - - +
70L ILE* 5.0 2.0 - - + +
72L LEU* 4.9 2.2 - - - -
73L ILE* 3.7 32.3 - - + -
77L LEU* 4.4 4.3 - - - -
108L GLY 3.2 17.6 + - - -
109L ILE 3.5 9.0 - - - +
110L GLU 3.2 0.2 - - - -
111L TYR* 1.3 76.7 - - - +
113L LYS* 1.3 55.4 + - - +
114L GLU 3.0 6.7 + - - -
115L ASN* 3.5 5.9 + - - +
116L SER* 3.2 28.3 + - - -
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Residues in contact with LYS 113 (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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70L ILE* 6.2 0.2 - - - -
109L ILE* 3.3 26.2 + - - +
110L GLU* 3.1 21.7 + - + +
112L CYS* 1.3 75.0 - - - +
114L GLU* 1.3 60.0 + - - +
116L SER* 3.5 15.5 + - - +
120L PRO* 3.7 38.3 - - + +
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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