Contacts of the helix formed by residues 76 - 97 (chain J) in PDB entry 5T0G
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 LEU 76 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I PHE* 5.7 6.1 - - + -
18I LEU* 5.4 13.9 - - + -
25J ALA* 5.0 15.4 + - + -
73J PHE* 4.9 0.2 - - - -
74J ALA 4.5 0.6 - - - +
75J GLY* 1.3 72.0 - - - -
77J THR* 1.3 64.1 + - - +
78J ALA* 4.0 10.3 - - + +
79J ASP* 3.2 43.7 - - + +
80J ALA* 4.2 1.4 - - - +
128J GLY* 5.3 4.0 - - - +
129J ILE* 3.2 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I ASN* 3.1 36.3 + - - +
60J ARG 5.9 0.7 - - - +
61J LYS* 3.5 31.9 - - + +
73J PHE* 3.7 20.1 - - + -
75J GLY 4.5 0.7 - - - +
76J LEU* 1.3 71.6 - - - +
78J ALA* 1.3 65.0 + - - +
79J ASP 3.3 0.2 - - - -
80J ALA* 3.0 2.5 + - - +
81J ARG* 3.0 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I GLN* 2.4 32.3 + - - +
153I SER* 3.3 29.2 - - - +
154I GLY* 3.8 3.1 - - - -
155I ASN* 3.6 18.8 - - + +
76J LEU* 3.3 11.3 - - + +
77J THR* 1.3 82.2 + - - +
79J ASP* 1.3 58.3 + - - +
81J ARG* 3.6 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 79 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I PHE* 5.0 5.5 - - - -
18I LEU* 6.2 0.2 - - - +
119I GLN* 3.2 6.1 + - - +
123I GLN* 2.6 31.1 + - - +
153I SER 5.6 0.3 - - - +
76J LEU* 3.2 25.3 - - + +
77J THR 3.3 0.2 - - - -
78J ALA* 1.3 78.2 - - - +
80J ALA* 1.3 62.7 + - - +
82J ILE* 3.6 5.7 + - - +
83J VAL* 3.4 22.2 + - - +
125J ARG* 4.2 9.3 + - - -
127J PHE* 3.9 20.9 - - + -
128J GLY 4.1 14.2 + - - -
129J ILE* 3.4 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J PHE* 3.5 46.4 - - + -
76J LEU 4.2 0.2 - - - +
77J THR 3.0 9.9 + - - +
79J ASP* 1.3 76.5 - - - +
81J ARG* 1.3 66.5 + - - +
83J VAL* 3.1 8.0 + - - +
84J ILE* 2.8 30.0 + - + +
129J ILE* 3.2 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I THR* 4.3 19.5 - - - +
115I CYS* 4.6 1.5 - - - +
116I ASP* 3.1 28.8 + - - +
119I GLN* 4.5 0.2 + - - -
154I GLY 2.9 27.3 + - - -
155I ASN* 3.0 24.9 + - - +
156I TYR* 3.3 29.0 - - - -
77J THR* 3.0 21.7 + - - -
78J ALA* 3.6 20.5 + - - +
79J ASP 3.4 0.2 - - - -
80J ALA* 1.3 74.8 - - - +
82J ILE* 1.3 63.2 + - - +
84J ILE* 3.2 15.2 + - + +
85J ASN* 3.0 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I ASP* 4.0 33.2 - - + +
119I GLN* 3.4 30.5 - - + +
120I ALA 6.3 0.2 - - - +
123I GLN* 5.3 2.7 - - - +
78J ALA 4.1 0.2 + - - -
79J ASP 3.6 8.2 + - - +
80J ALA 3.2 0.8 - - - -
81J ARG* 1.3 72.3 - - - +
83J VAL* 1.3 67.8 + - - +
85J ASN* 3.3 6.9 + - + +
86J ARG* 2.9 40.8 + - + +
127J PHE* 4.4 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J ASP 3.4 17.0 - - - +
80J ALA* 3.1 10.7 + - + +
82J ILE* 1.3 76.4 - - - +
84J ILE* 1.3 63.0 + - + +
86J ARG* 3.4 7.2 - - + +
87J ALA* 2.9 23.6 + - + +
111J ILE* 4.0 32.0 - - + +
127J PHE* 3.5 30.3 - - + -
129J ILE* 5.1 4.3 - - + -
131J ALA* 6.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J CYS* 3.8 34.8 - - + -
65J LEU* 4.2 4.2 - - + +
71J MET* 5.6 4.3 - - + -
73J PHE* 4.6 19.7 - - + -
80J ALA* 2.8 23.9 + - + +
81J ARG* 3.2 17.3 - - + +
83J VAL* 1.3 76.0 - - + +
85J ASN* 1.3 67.3 + - - +
87J ALA* 2.9 8.9 + - - +
88J ARG* 2.8 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 85 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I ASP* 3.8 20.8 + - - -
81J ARG* 3.0 29.0 + - - +
82J ILE* 4.0 7.1 - - + +
84J ILE* 1.3 81.4 - - - +
86J ARG* 1.3 63.4 + - - +
88J ARG* 3.1 22.0 + - - +
89J VAL* 3.0 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J ILE* 2.9 31.4 + - + +
83J VAL* 3.4 9.0 - - + +
85J ASN* 1.3 74.7 - - - +
87J ALA* 1.3 62.9 + - - +
89J VAL* 3.0 18.7 + - - +
90J GLU* 3.0 12.5 + - - +
110J TYR* 3.5 35.6 + - + -
111J ILE* 6.0 3.1 - - + -
114J LEU* 3.7 34.3 - - + +
124J ARG* 4.9 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J LEU* 3.3 29.6 - - + +
71J MET* 5.2 5.8 - - - -
83J VAL* 2.9 17.6 + - + +
84J ILE* 2.9 9.5 + - - +
86J ARG* 1.3 74.1 - - - +
88J ARG* 1.3 57.2 + - - +
90J GLU* 4.4 5.8 - - - +
91J CYS 2.8 24.4 + - - -
107J ILE* 3.8 1.9 - - + +
110J TYR* 4.9 0.2 - - - -
111J ILE* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J CYS* 5.9 1.4 - - - +
64J ALA 3.4 23.8 + - - -
65J LEU* 3.4 26.6 + - + +
84J ILE* 2.8 36.8 + - + +
85J ASN* 3.1 21.5 + - - +
87J ALA* 1.3 74.7 - - - +
89J VAL* 1.3 67.6 + - + +
91J CYS* 3.0 13.7 - - - -
92J GLN* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85J ASN* 3.0 16.5 + - + +
86J ARG* 3.6 9.0 - - - +
88J ARG* 1.3 76.3 - - + +
90J GLU* 1.3 63.2 + - - +
92J GLN* 3.2 6.8 + - + +
93J SER* 2.9 23.2 + - - -
110J TYR* 6.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J ARG 3.0 7.2 + - - +
87J ALA 4.0 5.2 - - - +
88J ARG 3.3 0.2 - - - -
89J VAL* 1.3 77.0 - - - +
91J CYS* 1.3 57.5 + - - +
93J SER* 2.5 28.1 + - - -
94J HIS* 2.9 13.3 + - - +
106J TYR* 2.8 39.6 + - + -
107J ILE* 3.7 14.4 - - + -
110J TYR* 3.2 64.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 91 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J LEU* 3.7 38.1 - - + -
66J ASP* 5.7 4.7 - - + -
87J ALA 2.8 16.7 + - - +
88J ARG* 3.0 30.7 - - - -
90J GLU* 1.3 77.5 - - - +
92J GLN* 1.3 67.4 + - - +
94J HIS* 3.5 4.3 + - - +
95J ARG* 2.9 26.3 + - - +
102J VAL* 3.9 20.1 - - + +
107J ILE* 4.1 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J ARG* 2.9 23.5 + - - +
89J VAL* 3.7 6.1 - - - +
90J GLU 3.2 0.2 - - - -
91J CYS* 1.3 83.1 - - - +
93J SER* 1.3 59.2 + - - +
95J ARG* 3.6 23.1 - - - +
96J LEU* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89J VAL* 2.9 13.2 + - - -
90J GLU* 2.5 39.9 + - - -
92J GLN* 1.3 73.9 - - - +
94J HIS* 1.3 63.3 + - - +
95J ARG 3.1 1.6 - - - -
96J LEU* 3.0 17.2 + - - -
97J THR* 3.1 22.4 + - - +
106J TYR* 5.1 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 94 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J GLU* 2.9 13.9 + - + +
91J CYS 3.8 4.7 - - - +
93J SER* 1.3 76.0 + - - +
95J ARG* 1.3 56.4 + - - +
97J THR* 2.7 21.7 - - - +
98J VAL* 2.8 28.7 - - + +
100J ASP* 3.5 16.6 + - - +
101J PRO 3.9 7.4 - - - -
102J VAL* 3.3 46.1 - - + +
103J THR* 4.0 9.6 - - + -
106J TYR* 3.3 47.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J ASP* 3.3 25.2 + - - -
68J ASN* 5.7 2.0 - - - +
91J CYS 2.9 17.8 + - - +
92J GLN* 3.6 24.7 - - - +
94J HIS* 1.3 75.7 - - - +
96J LEU* 1.3 64.5 + - - +
98J VAL 4.7 0.2 - - - -
99J GLU* 2.8 64.9 + - - +
100J ASP 3.3 9.8 + - - -
101J PRO* 3.4 29.9 - - - +
102J VAL* 3.8 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J GLN 2.9 18.7 + - - +
93J SER* 3.0 10.6 + - - +
95J ARG* 1.3 73.4 - - - +
97J THR* 1.3 86.8 + - + +
99J GLU* 2.7 28.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J SER* 3.1 12.4 + - - +
94J HIS* 2.7 31.4 - - - +
96J LEU* 1.3 93.8 - - + +
98J VAL* 1.3 71.3 + - - +
----------------------------------------------------------
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