Contacts of the helix formed by residues 67 - 80 (chain P) in PDB entry 1H2I
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 GLU 67 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P SER* 3.7 14.4 + - - +
65P TYR* 3.7 27.5 + - + -
66P ILE* 1.3 74.6 - - - +
68P GLY* 1.3 69.5 + - - +
69P HIS* 3.4 26.8 - - + +
70P ARG* 2.8 48.2 + - - +
71P VAL* 3.2 7.9 + - - +
152P LYS* 5.0 0.2 - - - +
167Q LEU* 5.3 2.9 - - + +
169Q LYS* 4.2 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66P ILE 3.5 3.0 + - - -
67P GLU* 1.3 71.0 - - - +
69P HIS* 1.3 63.3 + - - +
71P VAL* 3.0 6.4 + - - +
72P ILE* 2.9 31.8 + - - +
148P THR* 4.1 26.0 - - - +
152P LYS* 4.1 12.6 - - - +
167Q LEU* 5.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P GLU* 3.0 37.5 + - + +
68P GLY* 1.3 74.9 - - - +
70P ARG* 1.3 79.9 + - + +
72P ILE* 3.5 0.8 + - - -
73P ASN* 3.2 20.8 + - - -
46Q ARG* 5.8 0.9 - - - -
164Q ASN* 2.9 52.1 - - - +
165Q CYS* 5.8 0.4 - - - -
167Q LEU* 3.1 36.8 - - + +
168Q ASP* 3.4 46.3 + - + -
169Q LYS 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195O ASP* 4.8 1.5 - - - +
50P GLU 3.9 15.7 + - - -
51P TYR* 3.8 43.0 + - + +
53P SER* 5.0 4.6 + - - -
66P ILE* 3.9 13.2 - - + -
67P GLU* 2.8 46.2 + - + +
69P HIS* 1.3 90.9 + - + +
71P VAL* 1.3 61.7 + - - +
73P ASN* 3.2 6.7 + - - +
74P LEU* 2.8 34.0 + - - +
168Q ASP* 4.1 6.9 + - - -
170Q ASP* 3.8 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66P ILE* 3.6 29.6 - - + -
67P GLU 3.8 6.3 - - - +
68P GLY 3.0 7.4 + - - +
70P ARG* 1.3 77.1 - - - +
72P ILE* 1.3 57.6 + - + +
74P LEU* 3.1 10.6 + - + +
75P ALA* 2.8 28.1 + - - +
151P LEU* 5.5 1.6 - - + -
152P LYS* 3.8 33.2 - - + -
155P LEU* 3.8 34.5 - - + -
156P ARG* 6.1 1.3 - - - +
162P LEU* 4.3 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68P GLY* 2.9 21.5 + - - +
69P HIS 3.8 5.2 - - - +
70P ARG 3.2 0.2 - - - -
71P VAL* 1.3 75.4 - - + +
73P ASN* 1.3 59.0 + - - +
75P ALA* 3.3 6.4 + - - +
76P ASN* 2.9 34.3 + - - +
84P TRP* 4.3 9.1 - - + -
148P THR* 6.6 0.4 - - + -
151P LEU* 4.4 22.2 - - + -
155P LEU* 5.9 0.4 - - + -
156Q ARG* 4.1 3.8 - - + +
157Q SER* 3.4 44.2 - - - +
164Q ASN* 3.6 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195O ASP* 3.2 24.8 + - + +
69P HIS* 3.2 17.6 + - - +
70P ARG* 3.2 4.8 + - - +
72P ILE* 1.3 74.1 - - - +
74P LEU* 1.3 68.2 + - - +
76P ASN* 3.9 12.2 + - - +
77P GLU* 2.9 31.9 + - + +
46Q ARG* 5.5 3.4 - - - +
159Q GLY* 4.3 1.0 - - - -
160Q ASN* 3.1 42.4 + - - +
164Q ASN* 3.2 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192O LYS* 3.9 23.8 - - + +
195O ASP* 4.0 5.9 + - - +
47P LEU* 3.5 25.8 - - + -
51P TYR* 3.8 37.0 - - + +
66P ILE* 5.0 5.6 - - + -
70P ARG 2.8 17.4 + - - +
71P VAL* 3.4 17.3 - - + +
73P ASN* 1.3 76.5 - - - +
75P ALA* 1.3 57.8 + - - +
77P GLU* 3.3 3.7 + - - +
78P MET* 2.8 34.3 + - + +
161P ALA 3.6 17.7 - - - +
162P LEU* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P VAL 2.8 13.6 + - - +
72P ILE* 3.5 6.3 - - - +
74P LEU* 1.3 77.2 - - - +
76P ASN* 1.3 57.6 + - - +
78P MET* 3.1 1.0 + - - -
79P PHE* 2.9 43.4 + - + +
84P TRP* 3.5 37.8 - - + -
155P LEU* 4.6 7.2 - - + -
162P LEU* 4.0 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 76 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P ILE* 2.9 28.5 + - - +
73P ASN* 3.4 8.6 + - - +
75P ALA* 1.3 74.8 - - - +
77P GLU* 1.3 59.4 + - + +
80P GLY* 2.7 33.7 + - - -
81P TYR* 3.6 19.0 - - - +
84P TRP* 2.9 19.8 + - - +
40Q GLN* 3.0 12.6 - - - +
121Q HIS* 4.9 0.3 - - - -
157Q SER 2.9 26.4 + - - +
158Q PHE 3.4 21.2 + - - +
159Q GLY* 3.7 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195O ASP* 3.5 40.4 - - + +
196O LEU* 3.5 13.3 - - - +
197O GLU* 4.4 13.0 + - - +
201O GLU* 5.3 1.2 - - - +
204O ARG* 2.8 21.3 + - - -
73P ASN* 2.9 22.4 + - + +
74P LEU 3.8 2.2 - - - +
76P ASN* 1.3 78.9 - - + +
78P MET* 1.3 60.2 + - - +
40Q GLN* 4.2 7.2 + - - +
44Q ARG* 2.6 56.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192O LYS* 4.4 4.9 - - - -
197O GLU* 4.0 21.0 - - + +
200O VAL* 3.5 10.8 - - - +
204O ARG* 3.2 15.8 + - - -
39P ILE* 3.7 15.6 - - + +
42P ALA* 3.6 34.1 - - + -
43P LEU* 3.7 27.6 - - + -
74P LEU* 2.8 19.8 + - + +
75P ALA 3.1 3.6 + - - +
77P GLU* 1.3 78.6 - - - +
79P PHE* 1.3 74.4 + - + +
161P ALA* 3.7 28.5 - - + -
162P LEU* 4.0 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81O TYR* 4.3 4.7 - + - -
204O ARG* 3.5 20.2 + - - +
31P TYR* 4.0 16.9 + - - +
35P GLU* 4.5 2.3 - - - +
39P ILE* 4.2 20.0 - - + -
43P LEU* 4.5 3.8 - - + -
75P ALA* 2.9 24.7 + - + +
78P MET* 1.3 100.7 - - + +
80P GLY* 1.3 61.4 + - - +
82P ASN* 4.4 0.7 + - - -
83P GLY* 3.2 32.9 - - - -
84P TRP* 3.9 15.3 - + + +
115P LEU* 4.1 26.2 - - + -
116P LYS* 4.9 3.1 + - - -
155P LEU* 4.9 3.4 - - + -
158P PHE* 4.1 31.2 - + + -
162P LEU* 4.6 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204O ARG* 3.6 16.3 - - - -
76P ASN 2.7 23.7 + - - -
79P PHE* 1.3 72.8 - - - +
81P TYR* 1.3 62.3 + - - -
82P ASN* 3.0 6.5 - - - -
83P GLY 2.8 15.6 + - - -
84P TRP* 3.5 12.6 - - - -
36Q TYR* 4.1 1.1 - - - -
40Q GLN* 3.4 11.7 - - - -
----------------------------------------------------------
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