Contacts of the helix formed by residues 84 - 98 (chain f) in PDB entry 5GJQ
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 THR 84 (chain f).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F GLU* 4.0 11.5 + - - +
49f LYS* 4.3 9.0 - - - +
50f THR* 4.6 1.3 - - - -
81f LYS* 6.3 3.6 - - - +
82f ALA 3.6 4.4 + - - +
83f MET* 1.3 77.8 - - - +
85f THR* 1.3 64.6 + - - +
86f GLY* 3.7 3.6 + - - -
87f ALA* 3.2 24.6 + - - +
88f ILE* 3.1 21.7 + - - +
113f LEU 5.7 0.4 - - - -
114f ASP* 6.1 1.8 - - - -
115f GLU* 3.6 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49f LYS* 3.5 8.0 + - - +
50f THR* 2.8 26.3 + - + -
84f THR* 1.3 73.2 - - - +
86f GLY* 1.3 64.1 + - - +
88f ILE* 3.1 4.0 + - - +
89f ALA* 2.9 26.2 + - - +
110f ILE* 3.6 27.7 - - + +
112f GLY* 4.3 12.3 - - - +
113f LEU 2.9 27.6 + - - -
114f ASP* 5.3 2.0 - - - +
120f ALA* 5.0 3.1 - - + -
122f TYR* 3.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F TYR 4.7 1.3 - - - -
104F ASN* 5.2 3.1 + - - +
84f THR* 3.4 4.3 + - - -
85f THR* 1.3 79.4 - - - +
87f ALA* 1.3 58.1 + - - +
89f ALA* 3.2 3.6 + - - +
90f ALA* 2.9 28.9 + - - +
114f ASP* 6.1 0.6 - - - +
122f TYR* 3.8 25.2 + - - -
130f TYR* 4.7 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F TYR* 3.5 23.0 - - + +
105F GLU* 3.5 19.5 - - + +
75f TYR* 5.1 0.4 - - - +
83f MET* 3.3 23.7 - - + +
84f THR* 3.2 26.9 + - - +
86f GLY* 1.3 77.4 - - - +
88f ILE* 1.3 57.4 + - - +
90f ALA* 3.4 2.1 + - - +
91f MET* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46f LEU* 3.8 31.4 - - + -
47f THR* 4.1 18.8 - - + -
50f THR* 4.1 13.2 - - + +
52f ILE* 6.1 0.2 - - + -
68f ILE* 4.9 9.2 - - + -
72f LEU* 3.5 25.6 - - + -
83f MET* 3.7 18.6 - - + -
84f THR 3.1 14.0 + - - +
85f THR* 3.1 8.7 + - - +
87f ALA* 1.3 73.0 - - - +
89f ALA* 1.3 60.7 + - - +
91f MET* 4.0 5.4 - - + +
92f LEU* 2.8 31.7 + - + +
110f ILE* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85f THR 2.9 13.0 + - - +
86f GLY* 3.4 10.1 - - - +
88f ILE* 1.3 75.6 - - - +
90f ALA* 1.3 56.6 + - - +
92f LEU* 3.2 5.0 + - - +
93f SER* 2.9 23.9 + - - -
110f ILE* 3.7 5.5 - - + +
122f TYR* 3.9 21.5 - - + -
124f PHE* 3.3 25.0 - - + -
130f TYR* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F PHE 5.4 0.4 - - - +
102F THR 3.2 20.2 - - - +
103F TYR 3.9 15.0 - - - +
104F ASN* 4.0 7.4 - - + -
57e ARG* 5.2 4.0 - - - +
86f GLY 2.9 15.3 + - - +
87f ALA 3.8 3.4 - - - +
89f ALA* 1.3 72.0 - - - +
91f MET* 1.3 66.5 + - - +
93f SER* 3.0 23.0 + - - -
94f THR* 3.1 8.0 + - - +
130f TYR* 3.9 18.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 91 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F THR* 3.3 9.1 + - + -
103F TYR* 3.1 45.5 - - + -
68f ILE* 4.8 16.6 - - + +
71f ARG* 3.5 50.7 - - + +
72f LEU* 4.9 2.5 - - + +
83f MET* 4.2 15.3 - - + -
87f ALA 2.9 12.4 + - - +
88f ILE* 4.0 7.4 - - + +
90f ALA* 1.3 77.1 - - - +
92f LEU* 1.3 62.9 + - - +
94f THR* 2.7 22.1 + - - -
95f ILE* 2.9 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52f ILE* 4.0 12.8 - - + -
64f LEU* 4.2 17.3 - - + -
68f ILE* 3.6 27.6 - - + -
88f ILE* 2.8 21.0 + - + +
89f ALA* 3.3 5.8 - - - +
91f MET* 1.3 78.8 - - + +
93f SER* 1.3 62.0 + - - +
95f ILE* 3.2 7.7 + - + -
96f LEU* 2.9 45.3 + - + +
108f ASN* 3.8 21.1 - - + +
110f ILE* 4.2 5.6 - - + -
124f PHE* 3.4 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54e PHE* 5.6 4.4 - - - -
89f ALA 2.9 7.6 + - - -
90f ALA* 3.1 11.2 - - - -
92f LEU* 1.3 75.8 - - - +
94f THR* 1.3 67.9 + - - +
96f LEU* 3.4 2.9 + - - +
97f TYR* 3.0 24.1 + - - +
124f PHE* 3.9 2.4 - - - -
128f GLY* 2.6 33.3 + - - -
130f TYR* 3.7 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F PHE* 4.3 23.6 - - + +
102F THR* 3.9 31.1 - - + +
54e PHE* 5.0 10.9 - - + -
57e ARG* 5.9 2.5 - - - -
71f ARG* 4.2 4.2 + - - -
90f ALA 3.1 10.7 + - - +
91f MET* 2.7 22.1 + - - +
93f SER* 1.3 81.0 - - - +
95f ILE* 1.3 59.5 + - - +
97f TYR* 3.2 5.5 + - - +
98f SER* 2.9 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64f LEU* 4.0 23.3 - - + -
67f ILE* 4.1 28.9 - - + -
68f ILE* 4.2 14.4 - - + -
71f ARG* 3.9 23.6 - - - +
91f MET* 2.9 41.5 + - + +
92f LEU* 3.6 8.7 - - + +
94f THR* 1.3 82.1 + - - +
96f LEU* 1.3 60.8 + - - +
98f SER* 2.7 25.2 + - - +
104f TYR* 3.8 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64f LEU* 4.1 25.4 - - + -
92f LEU* 2.9 24.1 + - + +
95f ILE* 1.3 78.0 - - - +
97f TYR* 1.3 61.4 + - - +
99f ARG* 3.3 19.2 + - - +
100f ARG* 4.0 0.5 + - - -
103f PRO* 5.6 0.3 - - - +
104f TYR* 3.8 27.5 + - + -
106f VAL 5.2 0.9 - - - +
108f ASN* 3.9 18.2 - - - +
124f PHE* 4.0 14.6 - - + -
125f ASP 3.7 13.2 - - - +
126f PRO* 3.8 14.6 - - + +
127f VAL* 3.9 10.1 - - - +
128f GLY* 3.7 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 97 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50e ALA* 4.0 17.7 - - + -
51e ASP* 2.6 33.3 + - - -
54e PHE* 3.2 61.9 - + + -
55e TRP* 3.3 23.9 + + - -
95e LEU* 3.3 12.5 - - - +
93f SER* 3.0 15.3 + - - +
94f THR 3.2 0.9 + - - +
96f LEU* 1.3 71.9 - - - +
98f SER* 1.3 66.6 + - - +
99f ARG 3.0 2.5 - - - -
100f ARG* 2.9 37.0 + - + +
101f PHE* 5.7 3.8 - + - -
127f VAL 3.1 21.7 + - - +
128f GLY 5.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54e PHE* 5.3 1.8 - - - -
94f THR 2.9 15.2 + - - -
95f ILE* 2.7 23.1 + - - +
97f TYR* 1.3 77.0 - - - +
99f ARG* 1.3 65.4 + - - +
100f ARG 3.3 1.4 + - - -
101f PHE* 6.0 1.0 - - - -
104f TYR* 5.1 0.3 - - - -
----------------------------------------------------------
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