Contacts of the helix formed by residues 74 - 85 (chain I) in PDB entry 1JJ2
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 ARG 74 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26750 A 4.1 31.6 + - - +
26760 C 2.9 25.4 + - - +
91B PRO 3.0 25.8 + - - -
92B TYR* 3.9 19.6 - - - +
73I LYS* 1.3 75.8 + - - +
75I PRO* 1.3 70.4 - - + +
76I ASP* 2.8 40.4 + - + +
77I GLY 3.3 3.2 + - - +
78I ILE* 3.0 22.5 + - - +
105I LEU* 3.6 9.8 - - - +
136I SER* 3.3 2.5 - - - -
141I ALA* 4.4 9.4 - - + +
142I ASN* 4.4 9.8 - - - +
144I THR* 3.9 7.5 - - - +
145I TRP* 4.4 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 75 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ALA* 3.8 6.6 - - - +
42I GLU* 3.7 24.5 - - + +
74I ARG* 1.3 83.8 - - + +
76I ASP* 1.3 63.1 + - - +
78I ILE* 4.0 9.2 - - + -
79I PHE* 3.4 21.8 + - - +
105I LEU* 3.3 23.1 - - + -
132I LEU* 3.7 29.6 - - + +
133I GLY* 4.6 0.2 - - - -
136I SER* 2.9 23.9 - - - +
145I TRP* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 76 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28150 G 4.7 5.4 + - - +
92B TYR* 3.9 16.6 + - - -
41I ALA* 4.8 3.6 - - - -
74I ARG* 2.8 38.9 + - + +
75I PRO* 1.3 85.0 - - - +
77I GLY* 1.3 62.3 + - - +
79I PHE* 3.6 3.3 + - - +
80I LYS* 3.4 15.0 + - - +
103I VAL* 3.2 36.6 - - - +
104I TYR* 4.1 4.9 - - - -
105I LEU* 3.8 17.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26760 C 5.9 0.2 - - - -
72I PRO* 3.6 20.4 - - - -
74I ARG* 3.3 4.8 + - - +
76I ASP* 1.3 76.7 - - - +
78I ILE* 1.3 67.6 + - - +
79I PHE 3.1 2.2 - - - -
80I LYS* 2.9 7.8 + - - -
81I ARG* 2.7 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12420 A 4.8 0.2 + - - -
19I MET* 3.4 19.7 - - + -
57I TYR* 3.8 26.9 - - + -
71I TYR* 3.4 22.1 + - + +
72I PRO* 2.8 36.3 - - - +
73I LYS* 4.0 7.4 - - - +
74I ARG 3.0 22.2 + - - +
75I PRO* 4.1 8.3 - - + +
77I GLY* 1.3 74.0 - - - +
79I PHE* 1.3 53.5 + - - +
81I ARG* 3.4 2.6 + - - +
82I THR* 2.7 36.8 + - - +
132I LEU* 4.6 8.1 - - + +
135I ILE* 5.5 4.9 - - + -
136I SER* 4.6 1.8 - - - +
139I LEU* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ALA* 3.7 23.8 - - + -
19I MET* 3.4 44.6 - - + +
22I VAL* 3.9 22.4 - - + -
23I ALA* 4.1 9.0 - - + -
38I VAL* 3.8 9.9 - - + -
41I ALA* 4.2 11.4 - - + -
44I ALA* 3.8 11.9 - - + -
75I PRO 3.4 14.8 + - - +
76I ASP 3.8 3.4 - - - +
77I GLY 3.1 0.6 - - - -
78I ILE* 1.3 80.1 - - - +
80I LYS* 1.3 62.1 + - - +
82I THR* 3.1 2.4 + - - -
83I ILE* 3.0 38.5 + - + +
103I VAL* 3.9 11.0 - - + -
132I LEU* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28150 G 2.6 55.8 + - + +
76I ASP 3.4 8.2 + - - +
77I GLY* 2.9 11.3 + - - +
79I PHE* 1.3 75.4 - - - +
81I ARG* 1.3 60.8 + - - +
83I ILE* 3.1 7.1 + - + +
84I ARG 2.9 23.6 + - - -
98I PHE* 3.4 44.3 + - + -
99I GLU* 5.4 2.0 + - - +
101I VAL* 3.0 28.7 + - + +
102I ARG* 4.1 0.2 - - - +
103I VAL* 3.8 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12410 G 4.5 1.4 + - - +
12420 A 5.4 2.9 - - - +
20810 A 4.5 13.9 + - - -
20820 G 3.2 15.6 + - - -
69I TYR* 4.7 5.3 + - - -
70I PHE* 2.9 45.0 + - - -
71I TYR* 4.0 30.1 - - + +
72I PRO* 4.1 13.6 - - + +
77I GLY 2.7 19.6 + - - +
78I ILE 3.7 4.0 - - - +
80I LYS* 1.3 73.1 - - - +
82I THR* 1.3 62.9 + - - +
84I ARG* 3.2 49.7 + - - +
85I GLY* 3.1 19.7 + - - +
98I PHE* 5.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 82 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12410 G 2.7 25.0 + - - +
12420 A 3.1 49.7 + - - -
19I MET* 3.5 24.8 - - + +
20I GLY* 4.8 0.2 - - - -
23I ALA* 3.8 20.6 - - + -
78I ILE* 2.7 19.7 + - - +
79I PHE* 3.2 11.9 - - - -
81I ARG* 1.3 77.7 - - - +
83I ILE* 1.3 61.5 + - - +
85I GLY 3.4 0.3 + - - -
86I MET* 3.9 6.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I ALA* 3.8 31.9 - - + +
26I VAL* 4.2 13.7 - - + -
27I ALA* 4.6 10.1 - - - +
38I VAL* 4.4 4.3 - - + -
79I PHE* 3.0 31.5 + - + +
80I LYS* 3.5 7.9 - - + +
82I THR* 1.3 75.6 - - - +
84I ARG* 1.3 56.3 + - - +
86I MET* 2.7 32.1 + - - +
87I LEU* 3.6 21.0 + - + +
98I PHE* 4.7 4.5 - - + -
101I VAL* 4.0 31.0 - - + -
103I VAL* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20810 A 2.7 31.1 + - - -
20820 G 2.9 28.8 + - - -
80I LYS 2.9 7.8 + - - +
81I ARG* 3.2 48.4 + - - +
83I ILE* 1.3 77.0 - - - +
85I GLY* 1.3 57.7 + - - +
87I LEU* 3.0 28.0 + - - +
89I HIS* 3.5 45.7 + - + -
98I PHE* 3.4 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11040 C 4.7 3.1 + - - +
12400 G 2.9 23.4 + - - +
12410 G 3.2 30.3 - - - +
20810 A 5.6 5.2 - - - -
81I ARG* 3.1 12.4 + - - -
82I THR 3.4 0.2 + - - -
83I ILE 3.1 1.6 - - - -
84I ARG* 1.3 76.2 - - - +
86I MET* 1.3 56.4 + - - +
87I LEU 3.3 3.5 + - - +
89I HIS* 5.6 1.8 - - - -
----------------------------------------------------------
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