Contacts of the helix formed by residues 56 - 72 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 4.4 18.9 + + - -
58A PHE* 6.0 1.6 - - - +
87A ASN* 5.6 2.5 - - - -
438A PHE* 4.9 0.9 - + - -
468A SER* 3.7 20.6 - - - +
469A ASN* 6.2 0.2 - - + -
1501A K 3.5 21.6 - - - -
33B VAL* 4.1 3.8 - - - -
54B THR* 2.8 17.7 + - - -
55B ARG* 1.3 78.6 - - - +
57B GLU* 1.3 66.9 + - - +
58B PHE* 3.1 39.3 + - + +
59B THR* 3.3 12.6 + - - +
87B ASN* 3.4 42.4 + - + -
469B ASN* 4.3 10.0 + - - +
471B SER* 6.4 1.1 - - - -
472B ASP* 3.5 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A PHE* 4.0 5.7 - - - -
600A TP9 2.5 38.2 + - - +
33B VAL* 3.6 24.1 - - + +
56B HIS* 1.3 72.8 + - - +
58B PHE* 1.3 64.9 + - - +
60B ALA* 3.1 10.7 + - - +
61B GLY 3.0 19.4 + - - -
78B TRP 4.5 2.2 - - - +
79B ALA* 3.7 23.7 - - + +
84B GLY* 3.7 5.6 - - - +
87B ASN* 3.0 29.3 + - + -
88B LEU* 3.5 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 6.0 2.2 - - - +
87A ASN* 5.4 3.4 - - - +
56B HIS* 3.1 24.4 + - + +
57B GLU* 1.3 75.9 - - - +
59B THR* 1.3 63.0 + - - +
61B GLY* 3.2 1.6 + - - -
62B VAL* 3.0 48.6 + - + +
87B ASN 3.8 10.6 + - - +
90B THR* 3.6 28.5 - - + -
91B GLY* 3.9 7.1 - - - +
94B THR* 4.0 4.5 - - - -
437B SER* 3.3 32.5 - - - -
438B PHE 3.9 7.0 - - - -
439B GLY* 3.5 27.4 - - - -
440B TYR* 4.0 10.5 - - + -
443B PRO* 4.3 4.0 - - + -
469B ASN* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B THR* 3.8 11.0 - - + -
56B HIS* 3.3 7.8 + - - +
57B GLU 3.2 0.6 - - - -
58B PHE* 1.3 77.7 - - - +
60B ALA* 1.3 57.5 + - - +
63B ALA* 2.9 30.8 + - + +
443B PRO* 3.3 23.4 - - + +
446B ILE* 4.1 15.3 - - + -
469B ASN* 3.0 23.2 + - - -
472B ASP* 2.7 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 3.5 21.4 - - + +
32B GLY* 3.4 38.4 - - - +
54B THR* 3.5 13.2 + - - +
56B HIS 3.6 2.0 + - - -
57B GLU* 3.1 12.5 + - - +
59B THR* 1.3 81.0 - - - +
61B GLY* 1.3 61.0 + - - +
63B ALA* 3.6 0.6 + - - -
64B ALA* 3.2 20.3 + - - +
77B CYS* 3.7 5.4 - - + +
88B LEU* 4.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU 3.0 13.3 + - - -
58B PHE 3.2 2.6 + - - -
60B ALA* 1.3 74.7 - - - +
62B VAL* 1.3 58.0 + - - +
64B ALA* 3.5 4.0 + - - +
65B ASP* 3.0 26.5 + - - +
77B CYS* 3.9 20.9 - - - -
88B LEU* 4.1 3.1 - - - +
91B GLY* 4.1 21.6 - - - +
102B VAL* 4.7 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PHE* 3.0 48.8 + - + +
61B GLY* 1.3 75.0 - - - +
63B ALA* 1.3 58.6 + - - +
65B ASP* 3.2 7.0 + - - +
66B VAL* 3.0 29.1 + - + +
91B GLY* 4.3 1.3 - - - -
94B THR* 3.9 20.2 - - + +
440B TYR* 3.6 31.6 - - + -
443B PRO* 3.6 26.0 - - + -
444B ALA 4.0 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 3.8 30.9 - - + -
54B THR* 5.8 0.9 - - + -
59B THR* 2.9 20.6 + - + +
60B ALA 3.9 0.9 - - - +
62B VAL* 1.3 74.9 - - - +
64B ALA* 1.3 58.0 + - - +
66B VAL* 3.5 0.4 + - - -
67B LEU* 3.0 31.2 + - - +
443B PRO* 3.6 22.6 - - + +
446B ILE* 4.3 10.8 - - + -
447B GLY* 3.9 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 4.1 10.2 - - + -
60B ALA 3.2 18.5 + - - +
61B GLY 3.6 4.5 - - - +
63B ALA* 1.3 77.4 - - - +
65B ASP* 1.3 56.3 + - - +
67B LEU* 4.5 0.2 - - - -
68B ALA* 2.9 30.8 + - - +
75B GLN* 3.4 15.1 - - + +
76B ALA 3.8 29.8 - - - +
77B CYS* 4.1 4.7 - - + -
102B VAL* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLY 3.0 14.1 + - - +
62B VAL* 3.4 11.1 - - - +
64B ALA* 1.3 76.3 - - - +
66B VAL* 1.3 64.6 + - - +
68B ALA* 3.3 4.3 + - - +
69B ARG* 2.8 62.1 + - - +
91B GLY 5.1 0.4 - - - +
94B THR* 3.9 20.7 - - + +
95B SER* 3.5 18.3 + - - -
98B ASP* 4.8 0.2 - - - +
100B SER* 2.5 30.8 + - - +
102B VAL* 3.6 7.3 - - + +
440B TYR* 4.1 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 3.0 20.3 + - + +
63B ALA 4.1 2.9 - - - +
65B ASP* 1.3 77.1 - - - +
67B LEU* 1.3 65.8 + - - +
69B ARG* 3.2 10.4 + - + +
70B ILE* 3.0 27.7 + - + +
430B LEU* 3.6 22.9 - - + -
440B TYR* 3.4 26.7 - - + +
444B ALA* 3.5 38.8 - - + +
447B GLY* 3.9 1.3 - - - -
448B ALA 3.6 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LYS* 4.9 10.8 - - + -
31B PHE* 3.8 28.3 - - + -
63B ALA 3.0 18.8 + - - +
64B ALA 3.8 3.6 - - - +
66B VAL* 1.3 77.2 - - - +
68B ALA* 1.3 51.0 + - - +
70B ILE* 3.5 0.3 + - - +
71B THR* 2.8 51.7 + - + +
75B GLN* 3.6 27.6 - - + +
447B GLY* 4.0 10.3 - - - +
450B MET* 4.4 8.7 - - + +
451B ALA* 3.7 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA 2.9 19.5 + - - +
65B ASP* 3.5 4.9 - - - +
67B LEU* 1.3 74.6 - - - +
69B ARG* 1.3 59.2 + - - +
72B GLY* 2.8 30.7 + - - -
73B ARG 3.3 23.6 + - - +
75B GLN* 3.4 7.7 - - + +
100B SER* 4.2 3.1 - - - -
101B PRO* 3.7 35.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP* 2.8 50.1 + - - +
66B VAL* 3.5 19.7 - - - +
68B ALA* 1.3 79.1 - - - +
70B ILE* 1.3 63.1 + - + +
72B GLY* 3.8 5.2 + - - -
98B ASP* 3.2 33.9 + - - +
99B ARG 3.5 14.9 + - - +
100B SER* 3.8 5.0 - - - -
101B PRO* 5.5 1.3 - - - -
225B ALA* 5.9 0.4 - - - +
229B ARG* 5.9 4.6 - - + +
252B ILE* 3.6 30.9 - - - +
427B PHE* 3.4 39.3 - - + -
430B LEU* 4.7 9.6 - - - +
431B THR 6.0 1.1 - - - -
440B TYR* 4.0 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 3.0 18.0 + - + +
69B ARG* 1.3 81.0 - - + +
71B THR* 1.3 61.4 + - + +
427B PHE* 4.3 22.5 - - + -
430B LEU* 4.0 20.2 - - + -
448B ALA* 3.8 30.3 - - + -
451B ALA* 3.7 24.7 - - + +
452B ARG* 3.8 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 2.8 47.0 + - + +
70B ILE* 1.3 76.9 - - + +
72B GLY* 1.3 61.7 + - - +
73B ARG* 3.2 56.8 + - - +
75B GLN* 3.3 15.1 + - - +
451B ALA* 4.6 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA 2.8 17.7 + - - -
69B ARG 3.8 5.1 + - - -
70B ILE 3.4 3.2 + - - -
71B THR* 1.3 74.1 - - - +
73B ARG* 1.3 59.7 + - - +
101B PRO* 5.1 4.5 - - - -
157B MET* 4.0 19.2 - - - +
191B PRO 5.2 0.3 - - - +
192B ALA 4.4 9.4 - - - +
193B LYS* 5.4 1.2 - - - -
194B PRO* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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