Contacts of the helix formed by residues 82 - 99 (chain D) in PDB entry 2IHU
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 GLY 82 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D LEU* 1.3 72.0 - - - +
83D PRO* 1.3 66.1 - - - +
85D MET* 3.1 17.2 + - - +
86D THR 3.1 21.3 + - - -
107D ALA 4.8 0.2 + - - -
108D GLN* 5.3 1.0 + - - -
121D GLN 3.2 17.2 + - - -
123D LEU* 3.7 28.4 - - - +
125D SER* 5.2 2.8 + - - -
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Residues in contact with PRO 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C THR* 3.8 6.7 - - + -
97C LEU* 5.8 0.4 - - + -
435C CYS* 3.3 45.0 - - - +
436C SER 4.1 0.2 - - - +
437C SER* 3.5 36.3 - - - +
600C TP8 3.9 7.2 - - + +
81D LEU 3.2 7.4 - - - +
82D GLY* 1.3 80.3 - - - +
84D GLY* 1.3 63.3 + - - +
86D THR* 3.3 11.5 + - + +
87D ASN* 3.0 30.0 + - - +
121D GLN* 4.0 13.0 - - + +
123D LEU* 5.1 0.2 - - + -
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Residues in contact with GLY 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600C TP8 4.1 1.3 - - - +
57D GLU* 3.6 20.9 - - - +
79D ALA* 3.2 14.7 - - - +
80D THR* 3.5 22.1 - - - +
81D LEU 3.1 6.7 + - - -
83D PRO* 1.3 81.1 - - - +
85D MET* 1.3 56.7 + - - +
87D ASN* 3.6 2.3 - - - +
88D LEU 3.0 23.7 + - - -
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Residues in contact with MET 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ALA* 4.2 6.1 - - - -
80D THR 3.0 15.2 + - - +
81D LEU* 5.1 0.7 - - - -
82D GLY* 3.1 21.0 + - - +
84D GLY* 1.3 75.9 - - - +
86D THR* 1.3 77.6 + - + +
88D LEU* 3.3 5.1 + - + +
89D SER* 3.0 20.0 + - - -
92D ILE* 5.1 1.9 - - + +
106D ALA* 3.9 8.1 - - + -
107D ALA 5.4 0.2 - - - +
123D LEU* 3.9 14.6 - - + -
125D SER* 3.6 30.5 - - - +
128D ILE* 4.0 14.1 - - + -
129D VAL* 3.8 22.2 - - + -
165D PHE* 3.9 29.4 - - + -
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Residues in contact with THR 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C THR 4.0 7.3 - - - +
89C SER* 3.9 9.2 - - - +
90C THR* 2.7 31.5 + - - +
93C ALA* 4.4 4.3 - - + +
132C MET* 3.8 23.3 - - + -
82D GLY 3.1 3.2 + - - +
83D PRO* 3.3 15.6 + - - +
84D GLY 3.3 0.4 - - - -
85D MET* 1.3 85.0 - - + +
87D ASN* 1.3 61.9 + - - +
89D SER* 2.6 25.2 + - - -
90D THR* 4.1 1.7 + - - -
123D LEU* 3.6 30.5 - - + -
128D ILE* 4.9 1.3 - - + -
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Residues in contact with ASN 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C HIS* 5.5 1.9 - - - -
58C PHE* 5.2 5.6 - - - +
87C ASN* 5.4 0.7 - - - +
90C THR* 2.7 30.0 + - - +
437C SER* 4.5 4.4 + - - -
438C PHE* 4.3 2.2 + - - -
600C TP8 3.3 21.4 - - - +
56D HIS* 3.4 30.7 + - + -
57D GLU* 3.1 30.9 + - + +
58D PHE* 3.8 15.6 + - - +
83D PRO 3.0 15.6 + - - +
84D GLY 3.6 1.6 - - - +
86D THR* 1.3 77.2 + - - +
88D LEU* 1.3 60.2 + - - +
89D SER 3.3 0.9 + - - -
90D THR* 3.5 13.5 + - - -
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Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D GLU* 3.5 29.9 - - + +
60D ALA* 4.6 1.1 - - + -
61D GLY* 4.0 4.7 - - - +
77D CYS* 3.7 30.5 - - + -
78D TRP 4.2 8.7 - - - +
79D ALA* 3.8 12.3 - - + +
84D GLY 3.0 17.0 + - - +
85D MET* 3.3 6.7 + - - +
87D ASN* 1.3 76.0 - - - +
89D SER* 1.3 56.6 + - - +
91D GLY* 2.8 21.8 + - - -
92D ILE* 2.9 20.2 + - + -
104D ALA* 4.2 20.9 - - + -
105D LEU 3.8 23.6 - - - +
106D ALA* 4.9 4.3 - - + -
165D PHE* 5.2 1.3 - - + -
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Residues in contact with SER 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C THR* 3.9 16.8 + - - +
89C SER* 4.2 3.3 + - - -
128C ILE* 5.9 0.7 - - - +
85D MET* 3.0 14.1 + - - -
86D THR* 2.6 23.9 + - - +
87D ASN 3.2 0.2 - - - -
88D LEU* 1.3 76.1 - - - +
90D THR* 1.3 52.2 + - - +
92D ILE* 3.5 13.4 - - - +
93D ALA* 2.7 34.0 + - - +
128D ILE* 5.4 5.1 - - - +
129D VAL* 4.9 7.9 - - - -
132D MET* 3.4 23.3 - - - +
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Residues in contact with THR 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PRO* 3.9 12.6 - - + -
86C THR* 2.8 30.7 + - - +
87C ASN* 2.7 31.9 + - - +
58D PHE* 3.6 26.2 - - + -
86D THR 4.5 0.7 + - - -
87D ASN* 3.5 9.3 + - - -
88D LEU 3.1 1.2 + - - -
89D SER* 1.3 76.6 + - - +
91D GLY* 1.3 58.7 + - - +
93D ALA* 3.6 2.9 + - - +
94D THR* 2.8 29.9 + - - -
435D CYS* 4.4 0.3 - - - -
437D SER* 3.8 12.3 - - - +
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Residues in contact with GLY 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D PHE* 3.9 7.7 - - - +
61D GLY* 4.1 28.9 - - - +
62D VAL* 4.2 9.6 - - - -
65D ASP* 5.0 0.2 - - - +
87D ASN 4.3 0.8 + - - -
88D LEU 2.8 9.8 + - - -
90D THR* 1.3 77.2 - - - +
92D ILE* 1.3 61.1 - - - -
94D THR* 3.2 9.4 + - - +
95D SER* 3.1 22.0 + - - -
102D VAL* 6.1 1.2 - - - +
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Residues in contact with ILE 92 (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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77D CYS* 5.4 1.6 - - - -
85D MET* 5.1 1.6 - - + +
88D LEU* 2.9 23.5 + - + +
89D SER* 3.2 23.5 + - - +
91D GLY* 1.3 75.2 - - - +
93D ALA* 1.3 57.6 + - - +
95D SER* 3.2 3.8 + - - -
96D VAL* 2.9 24.6 + - - +
102D VAL* 6.1 2.0 - - + -
104D ALA* 3.9 30.1 - - + -
129D VAL* 4.0 28.7 - - + -
132D MET* 3.6 23.3 - - + +
133D SER* 4.6 1.1 - - - -
163D PRO* 3.3 28.5 - - + +
165D PHE* 4.3 8.5 - - + -
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Residues in contact with ALA 93 (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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86C THR* 4.4 4.9 - - + +
123C LEU* 3.8 31.4 - - + -
89D SER 2.7 19.6 + - - +
90D THR* 3.8 8.7 - - - +
91D GLY 3.3 0.2 - - - -
92D ILE* 1.3 70.6 - - - +
94D THR* 1.3 65.4 + - - +
96D VAL* 3.4 11.6 - - - +
97D LEU* 3.1 27.0 + - - +
132D MET* 4.0 8.0 - - - -
435D CYS* 3.9 10.6 - - - +
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Residues in contact with THR 94 (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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58D PHE* 4.0 5.9 - - - -
62D VAL* 3.7 20.5 - - + +
65D ASP* 4.0 13.0 - - - +
90D THR 2.8 19.6 + - - -
91D GLY 3.3 10.3 - - - -
92D ILE 3.2 0.2 - - - -
93D ALA* 1.3 76.8 - - - +
95D SER* 1.3 56.1 + - - +
98D ASP* 2.8 54.1 + - - +
432D SER* 4.4 2.0 + - - +
435D CYS* 3.6 17.9 - - - +
437D SER* 4.5 2.9 - - - -
440D TYR* 3.9 22.9 - - + -
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Residues in contact with SER 95 (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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61D GLY 5.7 0.2 - - - -
65D ASP* 3.5 12.3 - - - -
91D GLY 3.1 12.7 + - - -
92D ILE* 3.5 8.3 - - - -
94D THR* 1.3 78.3 - - - +
96D VAL* 1.3 57.6 + - - +
99D ARG* 2.9 28.1 + - - -
100D SER* 2.7 36.0 + - - -
102D VAL* 3.7 12.8 - - - +
162D GLY* 3.9 1.7 - - - -
163D PRO* 3.3 21.5 - - - +
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Residues in contact with VAL 96 (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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117C ASN* 3.8 34.3 - - + +
123C LEU* 4.1 9.0 - - + -
92D ILE 2.9 7.0 + - - +
93D ALA* 3.4 19.3 - - - +
95D SER* 1.3 76.7 - - - +
97D LEU* 1.3 64.1 + - + +
99D ARG* 2.9 29.3 + - - +
132D MET* 3.2 35.4 - - + +
133D SER* 4.1 6.5 - - - +
134D LYS* 4.9 8.7 - - + -
161D VAL 4.5 1.9 - - - +
162D GLY* 4.5 1.3 - - - -
163D PRO* 3.5 16.1 - - + +
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Residues in contact with LEU 97 (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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82C GLY* 5.7 0.2 - - - -
117C ASN* 3.7 28.0 - - - +
118C ASP 4.1 0.2 - - - +
119C THR 3.6 23.8 - - - +
121C GLN* 4.0 13.5 - - - -
122C CYS 4.0 2.7 - - - +
123C LEU* 3.7 30.5 - - + -
93D ALA 3.1 10.3 + - - +
96D VAL* 1.3 84.0 - - + +
98D ASP* 1.3 63.5 + - - +
99D ARG* 3.7 7.6 + - - +
299D ALA* 3.5 28.2 - - + +
434D GLY* 3.7 19.7 - - - +
435D CYS* 3.6 26.5 - - + +
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Residues in contact with ASP 98 (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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65D ASP* 4.2 0.6 - - - +
69D ARG* 3.4 25.7 + - - +
94D THR* 2.8 35.6 + - - +
97D LEU* 1.3 69.2 - - - +
99D ARG* 1.3 76.6 + - - +
229D ARG* 4.9 1.7 + - - -
252D ILE* 4.8 8.9 - - + +
300D GLU* 6.2 0.2 - - - +
431D THR 4.9 1.1 - - - +
432D SER* 2.6 33.1 + - - -
433D ALA 4.2 1.6 - - - -
434D GLY 2.9 13.0 + - - +
435D CYS 2.8 29.3 + - - -
440D TYR* 4.1 4.2 + - - -
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Residues in contact with ARG 99 (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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117C ASN* 2.8 31.6 + - - +
118C ASP* 3.3 15.4 + - - +
69D ARG* 3.5 9.4 + - - +
95D SER 2.9 9.7 + - - -
96D VAL* 2.9 22.4 + - - +
97D LEU* 3.3 5.8 + - - +
98D ASP* 1.3 85.8 - - - +
100D SER* 1.3 63.0 + - - +
160D PRO* 3.8 27.4 - - - +
161D VAL* 3.1 36.6 - - + +
229D ARG* 4.0 25.7 + - - +
297D ASP* 2.7 43.0 + - - +
299D ALA* 3.6 12.2 - - + +
300D GLU* 6.5 0.4 - - + -
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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