Contacts of the helix formed by residues 94 - 113 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ASN* 6.1 0.4 - - - +
235C ASN 3.7 15.9 - - - -
236C LYS* 3.1 32.8 - - + -
237C ASN 4.4 0.2 - - - -
238C LEU 3.8 6.3 - - - -
239C ALA* 3.7 34.8 - - - +
240C HIS* 5.4 2.2 - + - -
417C PHE* 3.5 36.6 - + + -
418C GLU* 6.1 3.8 - - + -
88D TYR* 3.9 4.5 - - - -
91D GLY 4.3 11.9 - - - -
93D ILE* 1.3 82.1 - - - +
95D LEU* 1.3 69.1 + - - +
96D PRO* 3.4 8.5 - - + -
97D ASN* 3.0 29.7 + - - +
98D VAL* 3.3 11.4 + - - +
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 4.4 16.4 - - + -
229C ILE* 5.0 2.0 - - + -
236C LYS 3.0 8.9 + - - -
237C ASN* 3.4 35.7 - - + +
88D TYR* 3.6 15.1 - - + +
94D PHE* 1.3 71.2 - - - +
96D PRO* 1.4 73.1 - - + +
98D VAL* 2.7 26.2 + - + +
99D MET* 2.9 31.0 + - + -
142D ILE* 3.4 48.7 - - + -
146D LEU* 4.7 7.0 - - + -
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Residues in contact with PRO 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C VAL 4.2 11.4 - - - +
177C LEU* 3.1 30.1 - - - +
178C ARG 4.1 0.2 - - - -
179C ASN* 3.3 39.7 - - - +
237C ASN 3.1 29.6 - - - +
238C LEU* 4.2 7.2 - - + +
239C ALA 5.6 0.4 - - - +
94D PHE* 3.7 8.7 - - + -
95D LEU* 1.4 82.0 - - + +
97D ASN* 1.3 54.8 + - - +
99D MET* 3.2 1.1 + - + +
100D MET* 2.9 34.3 + - - +
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Residues in contact with ASN 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ASN* 4.2 15.7 + - - +
417C PHE* 3.4 22.4 - - - -
48D PHE* 4.8 5.6 - - + +
84D VAL* 4.5 0.2 - - - +
93D ILE* 3.9 25.2 - - + +
94D PHE* 3.0 34.1 + - - +
95D LEU 3.0 0.8 - - - -
96D PRO* 1.3 77.2 - - - +
98D VAL* 1.3 59.9 + - - +
100D MET* 3.9 15.8 + - + +
101D SER* 3.0 28.6 + - - -
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Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D MET* 4.0 9.1 - - + +
84D VAL* 3.8 22.9 - - + -
85D ILE* 5.6 5.2 - - + -
88D TYR* 3.6 37.2 - - + -
93D ILE* 4.2 2.7 - - + -
94D PHE 3.6 13.5 - - - +
95D LEU* 2.7 18.2 + - + +
97D ASN* 1.3 69.4 - - - +
99D MET* 1.3 60.9 + - - +
101D SER* 3.2 3.1 + - - -
102D ALA* 2.8 28.4 + - + +
145D ALA* 5.7 2.9 - - + +
146D LEU* 4.5 20.6 - - + -
149D ALA* 4.9 7.6 - - + -
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Residues in contact with MET 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 3.1 46.7 - - + +
178C ARG* 3.7 35.7 - - + +
95D LEU* 2.9 32.5 + - + +
96D PRO 3.5 1.6 - - - +
98D VAL* 1.3 72.6 - - - +
100D MET* 1.3 67.1 + - - +
102D ALA* 3.1 6.1 + - + +
103D ASP* 3.0 31.5 + - - +
141D ASN* 5.0 8.3 - - + +
142D ILE* 5.3 3.4 - - - -
145D ALA* 3.7 30.5 - - + -
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Residues in contact with MET 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C ARG* 3.3 34.9 - - + +
179C ASN* 4.4 12.6 - - - +
49D GLU 3.9 20.9 - - - +
50D GLY* 3.6 22.6 - - - +
96D PRO 2.9 23.7 + - - +
97D ASN* 4.0 13.9 - - - +
99D MET* 1.3 73.4 - - - +
101D SER* 1.3 61.5 + - - +
103D ASP* 3.5 9.9 + - - +
104D ALA* 3.2 17.5 + - - +
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Residues in contact with SER 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 2.7 31.9 + - - +
48D PHE 3.5 7.8 + - - -
50D GLY* 4.1 1.2 + - - -
81D MET* 3.9 10.8 - - - +
84D VAL* 3.4 27.6 - - - +
97D ASN 3.0 19.3 + - - -
98D VAL 3.2 5.3 + - - -
99D MET 3.1 0.6 - - - -
100D MET* 1.3 79.7 - - - +
102D ALA* 1.3 57.3 + - - +
104D ALA* 3.3 3.5 + - - +
105D MET* 3.0 27.0 + - - +
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D MET* 3.9 13.7 - - + +
98D VAL* 2.8 19.2 + - + +
99D MET* 3.1 8.0 + - + +
101D SER* 1.3 68.5 - - - +
103D ASP* 1.3 62.4 + - - +
105D MET* 3.4 11.4 + - + +
106D LEU* 2.9 36.9 + - + +
145D ALA* 4.8 15.3 - - + +
148D ARG* 6.0 1.8 - - + -
149D ALA* 4.7 11.4 - - + +
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Residues in contact with ASP 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C TYR* 4.7 5.3 + - - -
178C ARG* 2.7 45.6 + - - +
52D GLU* 5.5 2.7 - - - +
99D MET* 3.0 17.3 + - - +
100D MET* 3.5 11.3 - - - +
102D ALA* 1.3 78.2 - - - +
104D ALA* 1.3 61.2 + - - +
106D LEU* 3.5 8.7 + - - +
107D GLU* 3.3 24.1 + - - +
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 4.7 4.5 - - - +
50D GLY* 3.9 25.4 - - - +
51D GLU 4.1 1.1 - - - +
52D GLU* 4.0 24.6 - - + +
55D VAL* 3.7 24.9 - - + +
100D MET 3.2 14.1 + - - +
101D SER* 3.7 5.4 - - - +
102D ALA 3.3 0.2 - - - -
103D ASP* 1.3 78.1 - - - +
105D MET* 1.3 62.4 + - - +
107D GLU* 3.8 3.1 + - - +
108D GLY 3.4 13.3 + - - -
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Residues in contact with MET 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 4.2 16.1 - - + +
77D LEU* 4.0 26.1 - - + +
78D MET* 4.7 9.9 - - - +
81D MET* 3.9 28.3 - - - +
101D SER 3.0 16.6 + - - +
102D ALA* 3.7 13.9 - - + +
104D ALA* 1.3 74.6 - - - +
106D LEU* 1.3 86.1 + - + +
108D GLY* 2.7 22.0 + - - -
109D ILE* 2.8 27.7 + - + +
148D ARG* 4.3 26.0 - - + +
149D ALA* 4.7 2.0 - - - +
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ALA* 2.9 22.0 + - + +
103D ASP* 3.5 8.9 + - - +
105D MET* 1.3 92.8 - - + +
107D GLU* 1.3 57.0 + - - +
109D ILE* 3.4 17.5 + - + +
110D GLU* 3.1 30.2 + - - +
148D ARG* 4.6 35.4 - - + +
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Residues in contact with GLU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D GLU* 3.6 33.1 - - + +
53D ASP* 5.1 2.6 - - - +
56D VAL* 4.6 18.4 - - + +
103D ASP 3.3 14.0 + - - +
104D ALA 4.0 5.6 - - - +
105D MET 3.2 0.6 - - - -
106D LEU* 1.3 78.2 - - - +
108D GLY* 1.3 57.7 + - - +
110D GLU* 3.6 21.7 - - - +
111D TYR* 3.4 24.1 + - - +
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Residues in contact with GLY 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D VAL* 4.0 11.2 - - - -
56D VAL* 5.4 2.0 - - - -
59D LEU* 3.6 21.6 - - - +
77D LEU* 3.4 11.3 - - - +
104D ALA 3.4 4.6 + - - -
105D MET 2.7 8.2 + - - -
107D GLU* 1.3 78.4 - - - +
109D ILE* 1.3 60.0 + - - +
111D TYR* 3.8 2.1 + - - +
112D CYS* 3.2 28.8 + - - -
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Residues in contact with ILE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ILE* 4.1 27.8 - - + -
77D LEU* 3.7 15.5 - - + -
78D MET* 6.1 2.9 - - + -
105D MET* 2.8 40.3 + - + +
106D LEU* 3.4 19.9 + - + +
108D GLY* 1.3 73.8 - - - +
110D GLU* 1.3 61.1 + - + +
111D TYR 3.0 4.0 - - - -
112D CYS* 2.8 24.1 + - - +
113D LYS* 2.9 31.6 + - + +
120D PRO* 5.3 3.6 - - + -
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Residues in contact with GLU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU 3.1 16.2 + - - +
107D GLU* 3.6 25.2 - - - +
109D ILE* 1.3 78.5 - - - +
111D TYR* 1.3 62.2 + - - +
113D LYS* 3.5 31.9 - - + +
114D GLU* 3.5 39.9 - - - +
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Residues in contact with TYR 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D VAL* 4.0 26.0 - - + -
59D LEU* 4.4 25.6 - - + -
60D GLN* 3.0 39.5 + - + +
63D ILE* 4.6 14.3 - - + +
107D GLU 3.4 19.4 + - - +
108D GLY* 3.9 6.7 - - - +
109D ILE 3.0 0.4 - - - -
110D GLU* 1.3 75.5 - - - +
112D CYS* 1.3 64.6 + - - +
113D LYS 3.3 0.2 - - - -
114D GLU* 3.5 19.6 + - - +
115D ASN* 2.9 42.9 + - - -
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Residues in contact with CYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU* 4.2 22.4 - - - -
69D PRO 4.0 20.7 - - - +
70D ILE* 4.9 3.3 - - - +
72D LEU* 4.6 1.3 - - - -
73D ILE* 3.8 35.0 - - + -
77D LEU* 4.5 2.0 - - - -
108D GLY 3.2 20.8 + - - -
109D ILE 2.8 7.6 + - - +
111D TYR* 1.3 77.6 - - - +
113D LYS* 1.3 51.8 + - - +
114D GLU 2.8 15.8 + - - -
115D ASN* 2.9 18.1 + - - +
116D SER* 3.2 13.0 + - - -
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Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ILE* 5.4 1.8 - - - +
109D ILE* 2.9 21.8 + - + +
110D GLU* 3.5 33.5 - - + +
111D TYR 3.3 0.6 - - - -
112D CYS* 1.3 74.3 - - - +
114D GLU* 1.3 58.3 + - + +
116D SER* 3.3 16.7 + - - -
117D GLY 5.0 1.0 + - - -
120D PRO* 4.2 29.8 - - + -
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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