Contacts of the helix formed by residues 94 - 113 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235O ASN 3.5 23.3 - - - -
236O LYS* 3.0 26.2 - - + +
237O ASN 4.3 0.2 - - - -
238O LEU* 3.6 8.7 - - - -
239O ALA* 3.5 34.1 - - - +
240O HIS* 5.9 1.8 - + - -
417O PHE* 3.4 37.5 - + + -
418O GLU* 6.2 3.4 - - + -
88P TYR* 3.9 4.7 - - - -
91P GLY 4.2 14.1 - - - -
93P ILE* 1.3 81.6 - - - +
95P LEU* 1.3 69.1 + - - +
96P PRO* 3.4 10.5 - - + -
97P ASN* 2.9 25.9 + - - +
98P VAL* 3.4 10.4 + - - +
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Residues in contact with LEU 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177O LEU* 4.3 24.2 - - + -
229O ILE* 4.9 4.3 - - + -
236O LYS 2.9 9.3 + - - -
237O ASN* 3.5 33.0 - - + +
88P TYR* 3.5 14.6 - - + +
94P PHE* 1.3 69.2 - - - +
96P PRO* 1.4 66.7 - - + +
98P VAL* 2.9 33.2 + - + +
99P MET* 2.9 31.9 + - + +
138P ILE* 5.2 0.7 - - + -
142P ILE* 3.7 47.1 - - + -
146P LEU* 5.7 0.4 - - + -
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Residues in contact with PRO 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176O VAL 4.2 15.0 - - - +
177O LEU* 3.4 19.9 - - - +
178O ARG 4.2 0.2 - - - -
179O ASN* 3.3 43.7 - - - +
237O ASN 3.2 21.1 - - - +
238O LEU* 4.3 6.3 - - + -
239O ALA 5.8 0.4 - - - +
94P PHE* 3.5 11.7 - - + -
95P LEU* 1.4 89.6 - - + +
97P ASN* 1.3 56.1 + - - +
99P MET* 3.1 2.6 + - - +
100P MET* 2.8 35.6 + - - +
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Residues in contact with ASN 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179O ASN* 4.4 13.2 + - - +
417O PHE* 3.6 18.7 - - - -
48P PHE* 5.0 5.7 - - + +
93P ILE* 3.6 27.3 - - + +
94P PHE* 2.9 36.8 + - - +
96P PRO* 1.3 74.0 - - - +
98P VAL* 1.3 63.5 + - - +
100P MET* 3.3 12.6 + - - +
101P SER* 2.9 28.5 + - - +
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Residues in contact with VAL 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81P MET* 3.8 12.8 - - + +
84P VAL* 3.9 20.2 - - + +
85P ILE* 5.4 4.5 - - + -
88P TYR* 3.6 39.7 - - + -
93P ILE* 4.2 3.8 - - + -
94P PHE 3.7 9.0 - - - +
95P LEU* 2.9 22.8 + - + +
97P ASN* 1.3 72.0 - - - +
99P MET* 1.3 54.4 + - + +
101P SER* 3.2 3.8 + - - -
102P ALA* 2.8 32.6 + - + +
145P ALA* 5.3 6.5 - - + -
146P LEU* 4.4 21.5 - - + -
149P ALA* 6.0 1.1 - - + -
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Residues in contact with MET 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177O LEU* 3.4 48.5 - - + +
178O ARG* 4.2 24.7 - - + +
95P LEU* 2.9 37.3 + - + +
96P PRO 3.6 1.3 - - - +
98P VAL* 1.3 73.0 - - - +
100P MET* 1.3 66.7 + - - +
101P SER 3.2 1.1 - - - -
102P ALA* 4.0 4.6 - - - +
103P ASP* 3.1 33.1 + - - +
141P ASN* 4.2 21.3 - - + +
142P ILE* 5.2 1.3 - - + -
145P ALA* 3.8 25.8 - - + -
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Residues in contact with MET 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178O ARG* 3.4 35.4 - - + +
179O ASN* 4.7 10.1 - - - -
49P GLU 4.4 15.9 - - - +
50P GLY* 3.6 26.6 - - - +
96P PRO 2.8 21.6 + - - +
97P ASN* 3.7 10.8 - - - +
99P MET* 1.3 75.3 - - - +
101P SER* 1.3 57.1 + - - +
103P ASP* 3.5 7.3 + - - +
104P ALA* 3.1 21.8 + - - +
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Residues in contact with SER 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P ILE* 2.9 28.4 + - - +
48P PHE 3.5 9.2 + - - -
50P GLY* 4.2 1.1 - - - -
81P MET* 4.0 9.2 - - - +
84P VAL* 3.5 31.3 - - - +
93P ILE* 5.5 0.3 - - - +
97P ASN 2.9 15.9 + - - -
98P VAL 3.3 8.1 - - - -
100P MET* 1.3 74.1 - - - +
102P ALA* 1.3 66.1 + - - +
104P ALA* 3.2 3.5 + - - +
105P MET* 3.0 24.1 + - - +
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Residues in contact with ALA 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P MET* 3.7 19.7 - - + +
98P VAL* 2.8 20.1 + - + +
99P MET* 3.5 7.6 + - - +
101P SER* 1.3 72.4 - - - +
103P ASP* 1.3 59.7 + - - +
105P MET* 3.7 10.7 - - + +
106P LEU* 2.9 36.0 + - + +
145P ALA* 4.5 24.2 - - + +
148P ARG* 6.2 2.0 - - + -
149P ALA* 5.8 0.2 - - + -
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Residues in contact with ASP 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174O TYR* 5.1 3.3 + - - -
178O ARG* 2.8 41.5 + - - -
52P GLU* 5.5 0.2 - - - -
99P MET* 3.1 22.2 + - - +
100P MET* 3.5 7.6 - - - +
102P ALA* 1.3 78.8 - - - +
104P ALA* 1.3 62.3 + - - +
105P MET 3.3 0.2 + - - -
106P LEU* 3.3 9.8 + - - +
107P GLU* 3.2 24.7 + - - +
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Residues in contact with ALA 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P ALA 4.6 1.6 - - - +
47P ILE* 4.8 2.2 - - - +
50P GLY* 3.8 26.5 - - - +
52P GLU* 3.9 25.2 - - - +
55P VAL* 3.7 25.3 - - + +
100P MET 3.1 14.0 + - - +
101P SER* 3.2 4.5 + - - +
103P ASP* 1.3 79.0 - - - +
105P MET* 1.3 59.9 + - - +
107P GLU* 3.6 4.5 + - - +
108P GLY 3.3 13.9 + - - -
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Residues in contact with MET 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P ILE* 4.2 15.9 - - + +
77P LEU* 4.1 27.9 - - + +
78P MET* 4.5 13.9 - - - +
81P MET* 3.9 27.6 - - - -
101P SER 3.0 16.8 + - - +
102P ALA* 3.7 14.4 - - + +
104P ALA* 1.3 73.6 - - - +
106P LEU* 1.3 84.3 + - + +
107P GLU 3.1 1.6 - - - -
108P GLY* 2.7 22.7 + - - +
109P ILE* 2.9 31.5 + - + +
148P ARG* 4.8 20.4 - - + +
149P ALA* 5.4 0.7 - - - +
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Residues in contact with LEU 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102P ALA* 2.9 19.9 + - + +
103P ASP* 3.8 8.3 - - - +
105P MET* 1.3 93.2 - - + +
107P GLU* 1.3 56.4 + - - +
109P ILE* 3.6 17.4 + - + +
110P GLU* 3.2 28.4 + - - +
113P LYS* 6.1 2.0 - - - +
148P ARG* 3.9 40.4 - - + +
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Residues in contact with GLU 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52P GLU* 3.6 32.5 - - + +
53P ASP* 4.8 2.1 - - - +
56P VAL* 4.3 16.0 - - + +
103P ASP 3.2 12.3 + - - +
104P ALA 3.6 10.5 - - - +
105P MET 3.1 0.8 - - - -
106P LEU* 1.3 74.2 - - - +
108P GLY* 1.3 64.4 + - - +
109P ILE 3.3 0.4 - - - -
110P GLU* 3.3 26.7 - - + +
111P TYR* 3.2 22.2 + - - +
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Residues in contact with GLY 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55P VAL* 4.0 19.0 - - - +
56P VAL* 4.9 1.3 - - - -
59P LEU* 3.9 6.9 - - - +
77P LEU* 3.7 16.2 - - - -
104P ALA 3.3 4.9 + - - -
105P MET 2.7 9.5 + - - -
107P GLU* 1.3 80.5 - - - +
109P ILE* 1.3 59.2 + - - -
111P TYR* 3.2 6.7 + - - +
112P CYS* 3.1 26.5 + - - -
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Residues in contact with ILE 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73P ILE* 4.4 30.0 - - + +
77P LEU* 4.1 15.3 - - + -
78P MET* 5.4 5.2 - - - -
105P MET* 2.9 43.1 + - + +
106P LEU* 3.6 19.3 + - + +
107P GLU 3.3 0.4 - - - -
108P GLY* 1.3 73.6 - - - +
110P GLU* 1.3 59.8 + - - +
111P TYR 3.1 1.6 - - - -
112P CYS* 3.0 7.8 + - - +
113P LYS* 3.0 44.4 + - + +
120P PRO* 5.2 5.4 - - + -
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Residues in contact with GLU 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P LEU 3.2 12.0 + - - +
107P GLU* 3.3 43.1 + - + +
109P ILE* 1.3 75.3 - - - +
111P TYR* 1.3 60.3 + - - +
113P LYS* 3.6 35.1 + - - +
114P GLU* 3.6 18.8 + - - +
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Residues in contact with TYR 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56P VAL* 3.6 40.2 - - + -
59P LEU* 4.3 20.4 - - + -
60P GLN* 3.0 34.9 - - + +
63P ILE* 5.0 8.7 - - + -
107P GLU 3.2 17.5 + - - +
108P GLY* 3.4 6.1 - - - +
109P ILE 3.1 0.8 - - - -
110P GLU* 1.3 78.9 - - + +
112P CYS* 1.3 53.9 + - - +
113P LYS 3.3 0.4 - - - -
114P GLU* 3.7 22.4 + - - +
115P ASN* 2.8 43.6 + - - -
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Residues in contact with CYS 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59P LEU* 4.2 22.0 - - - -
63P ILE* 5.8 4.5 - - - -
69P PRO 3.4 27.0 - - - +
70P ILE* 3.9 4.3 - - - +
72P LEU* 4.8 6.7 - - - -
73P ILE* 4.0 27.6 - - + -
77P LEU* 4.3 5.8 - - - -
108P GLY 3.1 15.8 + - - -
109P ILE 3.0 9.5 + - - +
111P TYR* 1.3 74.7 - - - +
113P LYS* 1.3 61.4 + - - +
114P GLU 3.2 2.2 - - - -
115P ASN* 3.5 6.3 + - - +
116P SER* 3.4 22.2 + - - -
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Residues in contact with LYS 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70P ILE* 5.5 0.2 - - - -
106P LEU* 5.8 2.4 + - - +
109P ILE* 3.0 25.4 + - + +
110P GLU* 3.6 32.9 - - + +
111P TYR 3.3 0.4 - - - -
112P CYS* 1.3 78.3 - - - +
114P GLU* 1.3 59.2 + - + +
115P ASN 3.3 0.2 - - - -
116P SER* 2.7 26.1 + - - +
120P PRO* 4.6 22.0 - - + -
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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