Contacts of the helix formed by residues 52 - 68 (chain B) in PDB entry 2HYM
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 THR 52 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.1 34.0 + - - -
47B PHE* 3.6 25.9 - - - +
48B GLN* 5.2 0.7 - - - -
49B LYS 4.9 0.4 - - - -
50B ALA 3.0 3.9 - - - +
51B GLU* 1.3 77.7 - - - +
53B ILE* 1.3 63.0 + - + +
54B PRO 3.5 0.7 - - - -
55B VAL* 3.4 10.0 + - - +
56B LEU* 2.9 43.1 + - + +
154B SER 5.2 5.8 + - - +
155B THR* 6.1 0.2 - - - -
158B GLN* 4.2 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B CYS* 4.4 1.8 - - - -
50B ALA* 2.9 38.9 + - + +
52B THR* 1.3 81.6 - - + +
54B PRO* 1.4 59.1 - - + +
56B LEU* 3.1 10.9 + - + +
57B HIS* 2.9 28.0 + - + +
95B LEU* 3.2 45.0 - - + +
98B CYS* 3.5 30.3 - - + -
99B VAL* 4.6 2.7 - - + -
105B VAL* 4.2 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ALA 3.5 4.9 - - - +
51B GLU 3.3 18.8 - - - +
53B ILE* 1.4 98.0 - - + +
55B VAL* 1.3 63.3 + - + +
57B HIS* 3.5 5.4 + - + +
58B GLU* 3.3 32.4 + - - +
99B VAL* 5.4 5.2 - - + -
105B VAL* 3.5 28.5 - - + +
106B THR* 5.5 8.3 - - + -
108B THR* 5.9 0.7 - - - +
112B LYS* 5.4 13.7 - - + +
116B ILE* 4.1 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU 5.0 0.2 - - - +
43B PHE* 3.4 30.3 - - + -
47B PHE* 4.8 7.0 - - + -
51B GLU 4.1 14.4 - - - +
52B THR* 3.6 14.4 - - - +
53B ILE 3.2 0.2 - - - -
54B PRO* 1.3 77.8 - - + +
56B LEU* 1.3 55.0 + - - +
58B GLU* 3.3 3.1 + - - +
59B MET* 2.7 35.3 + - - +
112B LYS* 4.7 5.4 - - - +
115B SER* 3.6 51.1 - - - +
116B ILE* 3.9 10.2 - - - +
119B VAL* 4.1 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.6 24.7 - - + -
52B THR* 2.9 37.8 + - + +
53B ILE* 3.5 9.2 - - + +
55B VAL* 1.3 76.7 - - - +
57B HIS* 1.3 55.6 + - - +
59B MET* 3.4 8.9 - - - +
60B ILE* 2.9 41.5 + - + +
95B LEU* 3.5 27.6 - - + -
151B PHE* 5.7 1.1 - - + -
154B SER* 4.1 3.1 - - - -
155B THR* 3.6 46.9 - - + +
158B GLN* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE* 2.9 14.8 + - + +
54B PRO* 3.7 9.0 - - + +
56B LEU* 1.3 76.7 - - - +
58B GLU* 1.3 83.1 + - - +
61B GLN* 3.0 36.2 + - + +
92B LEU* 3.1 51.4 - - + +
95B LEU* 3.7 12.3 - - + +
96B GLU* 2.7 42.3 + - + +
99B VAL* 5.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PRO* 3.3 22.1 + - - +
55B VAL 4.0 2.5 - - - +
57B HIS* 1.3 108.6 + - - +
59B MET* 1.3 64.8 + - - +
61B GLN* 3.3 13.5 + - + +
62B GLN* 3.1 26.8 + - - +
116B ILE* 3.6 41.5 - - + +
119B VAL* 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 3.9 17.9 - - + -
43B PHE* 3.6 29.6 - - + -
55B VAL 2.7 19.1 + - - +
56B LEU* 3.2 12.8 + - - +
58B GLU* 1.3 77.2 - - - +
60B ILE* 1.3 64.0 + - + +
62B GLN* 3.1 14.8 + - - +
63B ILE* 3.1 32.6 + - + +
119B VAL* 3.8 28.0 - - + -
123B PHE* 4.2 5.5 - - + -
147B ILE* 5.9 0.4 - - + -
150B SER* 3.9 15.9 - - - -
151B PHE* 4.5 9.0 - - + +
154B SER* 3.7 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR* 6.1 0.2 - - + -
56B LEU* 2.9 19.9 + - + +
59B MET* 1.3 75.0 - - + +
61B GLN* 1.3 56.5 + - - +
63B ILE* 3.1 15.3 + - + +
64B PHE* 2.7 32.9 + - - +
88B LEU* 3.7 32.5 - - + +
91B GLN* 3.6 25.4 - - + -
92B LEU* 3.7 24.0 - - + +
95B LEU* 3.6 28.9 - - + -
151B PHE* 4.7 15.5 - - + -
155B THR* 6.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B HIS* 3.0 26.1 + - + +
58B GLU* 3.3 26.9 - - + +
59B MET 3.1 0.2 - - - -
60B ILE* 1.3 78.7 - - - +
62B GLN* 1.3 62.5 + - + +
64B PHE* 3.6 13.7 + - - +
65B ASN* 3.1 24.8 + - - +
89B TYR* 5.9 3.6 + - - -
92B LEU* 3.8 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU 3.1 13.8 + - - +
59B MET* 3.1 11.1 + - - +
61B GLN* 1.3 78.3 - - + +
63B ILE* 1.3 59.7 + - - +
65B ASN* 3.4 10.1 + - - +
66B LEU* 2.8 32.7 + - - +
116B ILE* 6.5 0.7 - - + -
119B VAL* 5.0 2.0 - - + -
120B ARG* 3.8 32.8 + - + +
123B PHE* 3.7 42.1 - - + +
124B GLN* 5.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B MET* 3.1 31.6 + - + +
60B ILE* 3.1 15.2 + - + +
62B GLN* 1.3 75.5 - - - +
64B PHE* 1.3 52.7 + - - +
66B LEU* 3.3 0.8 + - - -
67B PHE* 2.8 61.5 + - + +
84B PHE* 4.0 22.0 - - + -
88B LEU* 4.0 6.5 - - + -
123B PHE* 3.4 23.8 - - + -
147B ILE* 4.4 9.0 - - + -
151B PHE* 3.6 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE 2.7 20.2 + - - +
61B GLN* 3.7 20.9 - - - +
63B ILE* 1.3 73.3 - - - +
65B ASN* 1.3 62.8 + - + +
67B PHE* 3.7 0.9 - - - +
68B SER* 2.8 46.3 + - - -
85B TYR* 3.9 27.2 - + + -
88B LEU* 3.6 34.7 - - + +
89B TYR* 3.6 39.5 - + - -
92B LEU* 4.8 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLN* 3.1 15.8 + - - +
62B GLN* 3.9 10.1 + - - +
64B PHE* 1.3 84.9 - - + +
66B LEU* 1.3 67.5 + - - +
68B SER* 3.3 11.1 + - - -
69B THR* 3.2 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLN 2.8 22.6 + - - +
63B ILE 3.7 4.0 - - - +
65B ASN* 1.3 78.5 - - - +
67B PHE* 1.3 69.3 + - + +
69B THR* 2.6 32.9 + - + +
72B SER* 2.8 8.8 + - - +
123B PHE* 3.8 28.9 - - + +
126B ILE* 4.7 10.5 - - + -
127B THR* 3.8 34.1 - - + +
130B LEU* 4.8 12.8 - - + -
140B TRP* 5.1 2.0 - - + -
143B VAL* 4.6 16.6 - - + -
147B ILE* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.8 26.9 - - + -
21B MET* 4.2 5.6 - - + -
63B ILE* 2.8 49.2 + - + +
64B PHE* 4.2 2.0 - - - +
66B LEU* 1.3 85.9 - - + +
68B SER* 1.3 57.1 + - - +
69B THR 3.1 6.6 + - - -
72B SER* 3.1 19.3 - - - -
73B SER* 3.8 2.3 + - - -
76B TRP* 3.6 40.6 - + - -
81B LEU* 3.9 17.6 - - + +
84B PHE* 3.7 17.0 - + + -
85B TYR* 3.1 16.0 + - + -
140B TRP* 5.6 2.0 - + - -
143B VAL* 4.7 9.6 - - + -
144B ARG* 5.6 2.7 - - + -
147B ILE* 4.3 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 2.8 35.2 + - - -
65B ASN* 3.3 7.8 + - - -
67B PHE* 1.3 74.6 - - - +
69B THR* 1.3 65.8 + - - +
70B LYS* 3.8 1.2 + - - +
73B SER* 3.9 5.7 + - - -
85B TYR* 3.4 28.4 + - - -
----------------------------------------------------------
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