Contacts of the helix formed by residues 56 - 72 (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 HIS 56 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C HIS* 4.4 18.5 + + - -
58C PHE* 6.0 2.8 - - - +
87C ASN* 5.7 2.0 - - - -
438C PHE* 4.8 1.1 - + - -
468C SER* 3.6 19.3 - - - +
1502C K 3.5 22.2 - - - -
33D VAL* 4.1 3.4 - - - -
54D THR* 2.8 19.4 + - - -
55D ARG* 1.3 80.8 - - + +
57D GLU* 1.3 66.3 + - - +
58D PHE* 3.1 36.8 + - + +
59D THR* 3.3 12.9 + - - +
87D ASN* 3.4 46.3 + - + -
469D ASN* 4.3 10.7 + - - +
471D SER* 6.4 0.7 - - - -
472D ASP* 3.4 9.8 + - - +
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C PHE* 4.0 6.8 - - - -
600C TP8 2.7 33.6 + - - -
33D VAL* 3.7 22.5 - - + +
54D THR* 4.5 0.4 - - - -
56D HIS* 1.3 71.0 + - - +
58D PHE* 1.3 66.4 + - - +
60D ALA* 3.1 10.2 + - - +
61D GLY* 3.0 19.4 + - - -
78D TRP 4.5 3.1 - - - +
79D ALA* 3.8 12.8 - - + -
84D GLY* 3.6 16.1 - - - +
87D ASN* 3.1 30.3 + - + -
88D LEU* 3.5 30.4 - - + +
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Residues in contact with PHE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C HIS* 6.0 2.7 - - - +
87C ASN* 5.4 4.3 - - - +
56D HIS* 3.1 24.2 + - + +
57D GLU* 1.3 77.3 - - - +
59D THR* 1.3 60.6 + - - +
61D GLY* 3.3 2.3 + - - -
62D VAL* 3.0 43.2 + - + +
87D ASN 3.8 11.8 + - - +
90D THR* 3.6 26.5 - - + -
91D GLY* 3.9 8.6 - - - +
94D THR* 4.0 3.6 - - - -
437D SER* 3.4 33.2 - - - -
438D PHE 4.0 4.3 - - - -
439D GLY 3.4 26.9 - - - -
440D TYR* 3.9 14.4 - - + -
443D PRO* 4.4 3.1 - - + -
469D ASN* 3.5 22.4 - - + -
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Residues in contact with THR 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D THR* 4.0 11.4 - - + -
56D HIS* 3.3 7.8 + - - +
57D GLU 3.2 0.4 - - - -
58D PHE* 1.3 77.5 - - - +
60D ALA* 1.3 56.2 + - - +
63D ALA* 2.9 29.6 + - + +
443D PRO* 3.2 35.2 - - + +
446D ILE* 4.1 10.1 - - + -
469D ASN* 3.1 22.5 + - - -
472D ASP* 2.6 43.7 + - + +
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Residues in contact with ALA 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PHE* 3.5 22.4 - - + +
32D GLY* 3.4 38.6 - - - +
54D THR* 3.7 13.1 + - - +
56D HIS 3.6 2.0 + - - -
57D GLU* 3.1 12.0 + - - +
59D THR* 1.3 79.2 - - - +
61D GLY* 1.3 61.7 + - - +
63D ALA 3.5 0.2 + - - -
64D ALA* 3.1 21.5 + - - +
77D CYS* 3.8 5.3 - - + +
88D LEU* 4.6 2.5 - - + -
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Residues in contact with GLY 61 (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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57D GLU 3.0 13.8 + - - -
58D PHE 3.7 2.7 - - - -
60D ALA* 1.3 75.6 - - - +
62D VAL* 1.3 58.1 + - - +
64D ALA* 3.4 3.6 + - - +
65D ASP* 3.0 26.3 + - - +
77D CYS* 3.9 21.1 - - - -
88D LEU* 4.0 3.7 - - - +
91D GLY* 4.1 20.9 - - - +
102D VAL* 4.6 3.7 - - - +
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Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D PHE* 3.0 49.5 + - + +
61D GLY* 1.3 73.6 - - - +
63D ALA* 1.3 59.7 + - - +
65D ASP* 3.2 6.4 + - - +
66D VAL* 2.9 30.5 + - + +
91D GLY* 4.2 2.2 - - - -
94D THR* 3.7 23.1 - - + +
440D TYR* 3.6 31.2 - - + -
443D PRO* 3.7 23.1 - - + -
444D ALA 4.0 7.9 - - - +
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PHE* 3.8 33.2 - - + -
59D THR* 2.9 21.6 + - + +
60D ALA 3.9 0.4 - - - +
62D VAL* 1.3 75.8 - - - +
64D ALA* 1.3 57.6 + - - +
67D LEU* 2.9 31.0 + - - +
443D PRO* 3.5 22.1 - - + +
446D ILE* 4.3 9.9 - - + -
447D GLY* 3.8 7.1 - - - +
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Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PHE* 4.0 9.3 - - + -
60D ALA 3.1 17.0 + - - +
61D GLY 3.6 5.2 - - - +
63D ALA* 1.3 74.7 - - - +
65D ASP* 1.3 60.1 + - - +
67D LEU* 3.5 0.8 + - - -
68D ALA* 2.9 31.4 + - - +
75D GLN* 3.5 8.3 - - + +
76D ALA 3.8 35.9 - - - +
77D CYS* 4.2 4.3 - - + -
102D VAL* 3.8 11.0 - - + -
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Residues in contact with ASP 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D GLY 3.0 15.8 + - - +
62D VAL* 3.4 10.0 - - - +
64D ALA* 1.3 77.5 - - - +
66D VAL* 1.3 65.1 + - - +
68D ALA 3.4 0.3 + - - -
69D ARG* 2.7 59.2 + - - +
91D GLY 5.0 0.2 - - - +
94D THR* 4.0 20.9 - - + +
95D SER* 3.5 17.4 + - - +
98D ASP* 4.8 0.2 - - - +
100D SER* 2.5 34.3 + - - +
102D VAL* 3.5 8.0 - - + +
440D TYR* 4.1 2.8 + - - -
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Residues in contact with VAL 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D VAL* 2.9 23.3 + - + +
63D ALA 4.1 2.5 - - - +
65D ASP* 1.3 80.6 - - - +
67D LEU* 1.3 66.6 + - - +
69D ARG* 3.2 10.6 + - + +
70D ILE* 3.0 29.4 + - + +
430D LEU* 3.7 23.1 - - + -
440D TYR* 3.6 20.9 - - + +
444D ALA* 3.5 39.0 - - + +
447D GLY* 4.4 1.6 - - - -
448D ALA 3.9 9.2 - - - +
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Residues in contact with LEU 67 (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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29D LYS* 4.8 11.0 - - + -
31D PHE* 3.7 27.1 - - + -
63D ALA 2.9 18.8 + - - +
64D ALA 3.8 4.0 - - - +
66D VAL* 1.3 75.9 - - - +
68D ALA* 1.3 57.4 + - - +
70D ILE* 4.1 0.3 - - - +
71D THR* 2.8 52.2 + - + +
75D GLN* 3.5 31.0 - - + +
447D GLY* 3.9 11.3 - - - +
450D MET* 4.4 8.5 - - + +
451D ALA* 3.8 28.5 - - + +
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Residues in contact with ALA 68 (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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64D ALA 2.9 19.6 + - - +
65D ASP 3.5 5.2 - - - +
67D LEU* 1.3 73.8 - - - +
69D ARG* 1.3 58.8 + - - +
72D GLY* 2.8 30.1 + - - -
73D ARG 3.4 23.2 + - - +
75D GLN* 3.4 7.5 - - + +
100D SER* 4.2 3.1 - - - -
101D PRO* 3.8 36.3 - - + +
102D VAL* 4.5 0.2 - - + -
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Residues in contact with ARG 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ASP* 2.7 50.8 + - - +
66D VAL* 3.2 18.5 + - - +
68D ALA* 1.3 79.3 - - - +
70D ILE* 1.3 64.3 + - + +
72D GLY* 3.7 6.1 + - - -
98D ASP* 3.4 31.2 + - - +
99D ARG 3.5 15.2 + - - +
100D SER* 3.7 5.9 - - - +
101D PRO* 5.5 1.1 - - - -
229D ARG* 6.0 2.2 - - - +
252D ILE* 4.0 19.1 - - - +
427D PHE* 3.5 50.5 - - + -
430D LEU* 4.8 10.3 - - - +
431D THR 5.9 2.5 - - - -
440D TYR* 4.0 8.0 + - - -
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Residues in contact with ILE 70 (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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66D VAL* 3.0 17.6 + - + +
69D ARG* 1.3 79.0 - - + +
71D THR* 1.3 61.7 + - + +
72D GLY 3.5 0.2 + - - -
427D PHE* 4.2 22.9 - - + -
430D LEU* 4.0 16.6 - - + -
448D ALA* 3.8 35.4 - - + +
451D ALA* 3.7 22.2 - - + +
452D ARG* 3.7 39.9 - - + +
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Residues in contact with THR 71 (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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67D LEU* 2.8 47.0 + - + +
70D ILE* 1.3 77.3 - - + +
72D GLY* 1.3 63.2 + - - +
73D ARG* 3.2 56.2 + - - +
75D GLN* 3.3 13.9 + - - +
451D ALA* 4.5 10.3 - - + +
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Residues in contact with GLY 72 (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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68D ALA 2.8 15.0 + - - -
69D ARG 3.7 5.1 + - - -
70D ILE 3.3 3.0 + - - -
71D THR* 1.3 77.8 - - - +
73D ARG* 1.3 60.9 + - - +
101D PRO* 5.1 4.9 - - - -
157D MET* 4.2 16.8 - - - +
191D PRO 5.1 0.9 - - - +
192D ALA 4.2 12.0 - - - +
193D LYS* 5.4 0.9 - - - -
194D PRO* 6.0 0.3 - - - +
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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
------------------------------------------------------------
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