Contacts of the helix formed by residues 67 - 80 (chain J) 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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J TYR 4.6 2.6 + - - -
53J SER* 3.7 21.4 + - - +
65J TYR* 3.7 19.3 + - + -
66J ILE* 1.3 75.6 - - - +
68J GLY* 1.3 68.7 + - - +
69J HIS* 3.1 28.6 - - + +
70J ARG* 2.7 45.1 + - - +
71J VAL* 3.2 7.7 + - - +
152J LYS* 5.0 0.4 - - - +
167K LEU* 5.3 2.5 - - + +
168K ASP* 5.5 0.2 - - - +
169K LYS* 4.3 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J ILE 3.5 3.2 + - - -
67J GLU* 1.3 69.9 - - - +
69J HIS* 1.3 63.2 + - - +
71J VAL* 2.9 16.0 + - - +
72J ILE* 2.9 22.4 + - - +
148J THR* 4.0 26.0 - - - +
152J LYS* 4.1 13.3 - - - +
167K LEU* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J GLU* 3.0 37.7 + - + +
68J GLY* 1.3 74.4 - - - +
70J ARG* 1.3 80.8 + - + +
72J ILE* 3.5 0.6 + - - +
73J ASN* 3.2 21.4 + - - -
46K ARG* 5.7 1.3 - - - -
160K ASN* 6.1 0.2 - - - -
164K ASN* 3.0 52.1 - - - +
165K CYS* 5.8 0.7 - - - -
167K LEU* 3.2 33.7 - - + +
168K ASP* 3.5 46.2 + - + -
169K LYS 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195I ASP* 4.3 1.8 - - - +
50J GLU 3.8 18.0 + - - -
51J TYR* 3.9 42.0 + - + +
53J SER* 5.0 4.9 + - - -
66J ILE* 3.9 13.0 - - + -
67J GLU* 2.7 48.7 + - + +
69J HIS* 1.3 92.5 + - + +
71J VAL* 1.3 57.0 + - - +
73J ASN* 3.2 6.7 + - - +
74J LEU* 2.8 32.8 + - - +
168K ASP* 4.2 6.7 + - - -
170K ASP* 3.8 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J ILE* 3.7 29.2 - - + -
67J GLU 3.8 4.9 - - - +
68J GLY* 2.9 7.7 + - - +
70J ARG* 1.3 75.3 - - - +
72J ILE* 1.3 67.3 + - + +
74J LEU* 3.3 10.9 + - + +
75J ALA* 2.9 22.2 + - - +
151J LEU* 5.6 1.8 - - + -
152J LYS* 3.8 33.9 - - + -
155J LEU* 3.9 33.4 - - + -
156J ARG* 6.1 1.1 - - - +
162J LEU* 4.2 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J GLY* 2.9 21.0 + - - +
69J HIS 3.8 4.7 - - - +
70J ARG 3.3 0.2 - - - -
71J VAL* 1.3 78.8 - - + +
73J ASN* 1.3 57.8 + - - +
75J ALA* 3.3 7.7 + - - +
76J ASN* 2.9 32.1 + - - +
84J TRP* 4.2 9.8 - - + -
148J THR* 6.5 1.1 - - + -
151J LEU* 4.5 22.0 - - + -
155J LEU* 6.3 0.2 - - + -
156K ARG* 4.2 3.1 - - + +
157K SER* 3.4 47.3 - - - +
164K ASN* 3.7 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195I ASP* 3.5 23.0 + - - +
69J HIS* 3.2 16.4 + - - +
70J ARG* 3.7 5.3 - - - +
72J ILE* 1.3 74.6 - - - +
74J LEU* 1.3 66.7 + - - +
76J ASN* 3.9 13.3 + - - +
77J GLU* 2.9 32.3 + - + +
46K ARG* 5.5 2.8 - - - +
159K GLY* 4.4 5.2 - - - -
160K ASN* 3.2 35.8 + - - +
164K ASN* 3.3 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192I LYS* 3.8 22.4 - - + +
195I ASP* 3.5 19.4 + - - +
47J LEU* 3.5 26.5 - - + -
51J TYR* 3.7 24.7 - - + +
66J ILE* 5.1 3.1 - - + -
70J ARG 2.8 20.9 + - - +
71J VAL* 3.3 16.6 + - + +
73J ASN* 1.3 76.4 - - - +
75J ALA* 1.3 59.3 + - - +
77J GLU* 3.3 2.9 + - - +
78J MET* 2.8 33.8 + - + +
161J ALA 3.5 17.0 - - - +
162J LEU* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J VAL 2.9 12.9 + - - +
72J ILE 3.4 8.5 - - - +
74J LEU* 1.3 74.8 - - - +
76J ASN* 1.3 67.1 + - - +
78J MET* 4.4 0.4 - - - -
79J PHE* 2.9 35.3 + - + -
84J TRP* 3.5 36.5 - - + -
155J LEU* 4.7 6.7 - - + -
162J LEU* 3.9 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J ILE* 2.9 27.5 + - - +
73J ASN* 3.4 8.4 + - - +
75J ALA* 1.3 75.6 - - - +
77J GLU* 1.3 60.9 + - + +
80J GLY* 2.6 34.7 + - - -
81J TYR* 3.6 18.8 - - - +
84J TRP* 2.8 25.2 + - - +
40K GLN* 3.0 13.1 - - - +
121K HIS* 4.9 0.5 - - - -
157K SER 3.1 24.3 + - - +
158K PHE* 3.3 22.6 + - - +
159K GLY* 3.7 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195I ASP* 3.5 41.1 - - + +
196I LEU* 3.3 15.9 - - - +
197I GLU* 4.7 8.4 + - - +
200I VAL* 4.6 2.6 - - - +
201I GLU* 5.3 3.5 - - - +
204I ARG* 2.8 20.4 + - - -
73J ASN* 2.9 23.7 + - + +
74J LEU 3.9 2.5 - - - +
76J ASN* 1.3 78.4 - - + +
78J MET* 1.3 59.9 + - - +
40K GLN* 4.1 8.1 + - - +
44K ARG* 2.5 55.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192I LYS* 4.4 14.8 - - - -
197I GLU* 4.5 9.6 - - + +
200I VAL* 3.3 18.5 - - - +
204I ARG* 3.1 13.0 + - - -
39J ILE* 3.7 12.8 - - + +
42J ALA* 3.7 32.5 - - + +
43J LEU* 3.8 27.1 - - + -
74J LEU* 2.8 19.6 + - + +
75J ALA 3.8 2.7 - - - +
77J GLU* 1.3 78.3 - - - +
79J PHE* 1.3 74.2 + - + +
161J ALA* 3.8 28.9 - - + -
162J LEU* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I TYR* 4.4 4.7 - + - -
204I ARG* 3.2 21.6 + - - +
31J TYR* 3.8 17.2 + - - +
35J GLU* 4.5 2.6 - - - +
39J ILE* 4.3 19.7 - - + -
43J LEU* 4.7 2.9 - - + -
75J ALA* 2.9 28.5 + - + +
78J MET* 1.3 96.5 - - + +
80J GLY* 1.3 61.7 + - - +
82J ASN* 4.4 0.9 + - - -
83J GLY* 3.3 32.2 - - - -
84J TRP* 3.9 16.2 - + + -
115J LEU* 3.9 32.1 - - + -
116J LYS* 4.9 2.8 + - - -
155J LEU* 5.0 2.9 - - + -
158J PHE* 4.0 30.1 - + + -
162J LEU* 4.6 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204I ARG* 3.5 13.5 - - - -
76J ASN 2.6 24.8 + - - -
79J PHE* 1.3 73.2 - - - +
81J TYR* 1.3 62.5 + - - -
82J ASN* 3.0 8.1 - - - -
83J GLY 2.8 16.3 + - - -
84J TRP* 3.5 12.6 - - - -
36K TYR* 4.0 3.8 - - - -
40K GLN* 3.3 10.3 - - - -
----------------------------------------------------------
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