Contacts of the helix formed by residues 67 - 80 (chain T) 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 T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51T TYR 4.6 2.2 + - - -
53T SER* 3.8 21.1 + - - +
65T TYR* 3.8 19.3 + - + -
66T ILE* 1.3 75.7 - - - +
68T GLY* 1.3 57.3 + - - +
69T HIS* 3.2 29.0 - - + +
70T ARG* 2.7 55.3 + - - +
71T VAL* 3.2 8.7 + - - +
152T LYS* 4.5 1.1 - - - +
167U LEU 5.3 2.1 - - - +
169U LYS* 4.2 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66T ILE 3.6 3.0 + - - -
67T GLU* 1.3 71.2 - - - +
69T HIS* 1.3 58.1 + - - +
71T VAL* 3.0 5.4 + - - +
72T ILE* 2.9 37.2 + - - +
148T THR* 4.0 25.5 - - - +
152T LYS* 4.1 12.6 - - - +
167U LEU* 5.8 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67T GLU* 3.1 38.3 + - + +
68T GLY* 1.3 75.1 - - - +
70T ARG* 1.3 80.7 + - + +
72T ILE* 3.8 0.7 - - - -
73T ASN* 3.2 21.5 + - - -
46U ARG* 5.9 1.1 - - - -
164U ASN* 3.1 49.1 - - - +
165U CYS* 5.8 0.2 - - - -
167U LEU* 3.1 37.5 - - + +
168U ASP* 3.5 46.0 + - + +
169U LYS 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195S ASP* 4.8 1.7 - - - +
50T GLU 3.9 17.0 + - - -
51T TYR* 3.8 42.0 + - + +
52T ILE 5.8 0.2 - - - -
53T SER* 4.9 4.4 + - - -
66T ILE* 3.8 13.5 - - + -
67T GLU* 2.7 45.6 + - + +
69T HIS* 1.3 93.5 + - + +
71T VAL* 1.3 60.3 + - - +
73T ASN* 3.2 7.0 + - - +
74T LEU* 2.8 33.7 + - - +
168U ASP* 4.2 5.7 + - - -
170U ASP* 3.9 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66T ILE* 3.6 31.0 - - + -
67T GLU 3.2 4.5 + - - +
68T GLY 3.0 7.5 + - - +
70T ARG* 1.3 75.1 - - - +
72T ILE* 1.3 59.3 - - + +
74T LEU* 3.2 11.4 + - + +
75T ALA* 2.9 28.2 + - - +
151T LEU* 5.5 2.0 - - + -
152T LYS* 3.9 31.9 - - + -
155T LEU* 3.8 33.7 - - + -
156T ARG* 6.1 1.1 - - - +
162T LEU* 4.3 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68T GLY* 2.9 22.4 + - - +
69T HIS 3.8 4.5 - - - +
71T VAL* 1.3 77.9 - - + +
73T ASN* 1.3 58.1 + - - +
75T ALA* 3.2 7.1 + - - +
76T ASN* 2.9 43.6 + - - +
84T TRP* 4.3 9.5 - - + -
148T THR* 6.5 0.7 - - + -
151T LEU* 4.4 23.6 - - + -
155T LEU* 6.0 0.2 - - - -
156U ARG* 4.1 3.8 - - + +
157U SER* 3.5 32.8 - - - +
164U ASN* 3.7 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195S ASP* 3.4 24.7 + - + +
69T HIS* 3.2 18.2 + - - +
70T ARG* 3.9 4.4 - - - +
72T ILE* 1.3 73.8 - - - +
74T LEU* 1.3 67.7 + - - +
76T ASN* 4.2 12.4 + - - +
77T GLU* 2.9 31.3 + - + +
46U ARG* 5.5 3.0 - - - +
159U GLY* 4.4 1.2 - - - -
160U ASN* 3.2 39.5 + - - +
164U ASN* 3.1 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192S LYS* 3.7 38.4 - - + -
195S ASP* 3.9 7.9 + - - +
47T LEU* 3.5 18.6 - - + -
51T TYR* 3.7 27.4 - - + +
66T ILE* 5.1 2.7 - - + -
70T ARG 2.8 21.4 + - - +
71T VAL* 3.2 17.0 + - + +
73T ASN* 1.3 77.1 - - - +
75T ALA* 1.3 58.3 + - - +
77T GLU* 3.7 2.7 - - - +
78T MET* 2.9 32.8 + - - +
161T ALA 3.5 21.3 - - - +
162T LEU* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71T VAL 2.9 16.8 + - - +
72T ILE 3.5 4.3 - - - +
74T LEU* 1.3 78.8 - - - +
76T ASN* 1.3 57.1 + - - +
78T MET* 4.4 0.4 - - - -
79T PHE* 2.9 41.1 + - + -
84T TRP* 3.5 37.4 - - + -
155T LEU* 4.7 7.6 - - + -
162T LEU* 4.0 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 76 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72T ILE* 2.9 29.3 + - - +
73T ASN* 3.9 9.1 + - - +
75T ALA* 1.3 76.1 - - - +
77T GLU* 1.3 61.7 + - + +
80T GLY* 2.7 34.4 + - - -
81T TYR* 3.6 17.9 - - - +
84T TRP* 2.7 24.8 + - - +
40U GLN* 3.1 12.9 - - - +
121U HIS* 4.9 0.3 - - - -
157U SER 3.0 26.1 + - - +
158U PHE* 3.5 19.8 + - - +
159U GLY* 3.8 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195S ASP* 3.4 41.5 - - + +
196S LEU* 4.1 14.0 - - - +
197S GLU* 4.5 8.9 + - - +
200S VAL* 4.4 3.6 - - - +
201S GLU* 5.3 1.7 - - - +
204S ARG* 3.1 18.4 + - - -
73T ASN* 2.9 22.6 + - + +
74T LEU 3.9 2.0 - - - +
76T ASN* 1.3 81.0 - - + +
78T MET* 1.3 59.2 + - - +
40U GLN* 4.0 8.1 + - - +
44U ARG* 2.6 55.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192S LYS* 4.3 8.5 - - - -
197S GLU* 4.3 14.6 - - + +
200S VAL* 3.4 18.5 - - - +
204S ARG* 3.4 12.2 + - - -
39T ILE* 3.8 16.4 - - + +
42T ALA* 3.8 31.2 - - + +
43T LEU* 3.9 26.9 - - + -
74T LEU* 2.9 18.2 + - + +
75T ALA 3.2 3.1 + - - +
77T GLU* 1.3 77.7 - - - +
79T PHE* 1.3 79.4 + - + +
161T ALA* 3.8 29.2 - - + -
162T LEU* 4.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81S TYR* 4.3 5.2 - + - -
204S ARG* 3.7 18.2 + - - +
31T TYR* 3.9 17.4 + - - +
35T GLU* 4.7 2.5 - - - +
39T ILE* 4.2 20.6 - - + -
43T LEU* 4.5 4.0 - - + -
75T ALA* 2.9 26.5 + - + +
78T MET* 1.3 99.2 - - + +
80T GLY* 1.3 60.8 + - - +
82T ASN* 4.3 1.2 + - - -
83T GLY* 3.2 33.4 - - - +
84T TRP* 3.9 15.5 - + + -
115T LEU* 4.1 26.0 - - + -
116T LYS* 4.9 2.9 + - - -
155T LEU* 5.0 2.5 - - + -
158T PHE* 4.1 31.9 - + + -
162T LEU* 4.5 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204S ARG* 3.7 14.8 - - - +
76T ASN 2.7 23.9 + - - -
79T PHE* 1.3 73.3 - - - +
81T TYR* 1.3 63.4 + - - -
82T ASN* 2.9 12.1 - - - -
83T GLY 2.9 10.9 + - - -
84T TRP* 3.5 12.5 - - - -
36U TYR* 4.1 2.0 - - - -
40U GLN* 3.4 11.0 - - - -
----------------------------------------------------------
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