Contacts of the helix formed by residues 96 - 109 (chain A) in PDB entry 1G8I
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 96 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 4.1 10.5 + - + +
94A ARG 5.7 0.2 - - - +
95A GLY* 1.3 76.7 - - - +
97A LEU* 1.3 59.9 + - - +
98A ASP* 3.7 8.4 + - - +
99A GLU* 3.1 38.6 + - - +
100A LYS* 2.9 27.3 + - - +
183A LEU 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A THR* 1.3 74.4 - - - +
98A ASP* 1.3 60.1 + - - +
100A LYS* 3.3 1.4 + - - +
101A LEU* 2.9 50.4 + - + +
174A LYS* 4.3 25.1 - - + +
179A ILE* 6.2 0.2 - - + -
180A VAL* 4.4 30.7 - - + +
183A LEU* 3.4 45.6 + - + +
184A SER* 4.7 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A THR* 3.3 7.2 + - - +
97A LEU* 1.3 76.5 - - - +
99A GLU* 1.3 63.5 + - - +
101A LEU* 3.4 7.8 + - - +
102A ARG* 3.2 51.1 + - - +
170A GLN* 5.3 2.8 - - - +
174A LYS* 2.7 38.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 2.7 38.3 + - - -
91A VAL* 3.6 23.6 - - + +
95A GLY* 3.5 0.9 - - - -
96A THR* 3.1 34.5 + - - +
98A ASP* 1.3 74.8 - - - +
100A LYS* 1.3 64.7 + - - +
102A ARG* 3.3 24.2 + - - +
103A TRP 3.2 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 3.4 23.8 - - - +
92A THR* 3.3 30.1 - - - +
93A SER 4.1 1.1 - - - -
95A GLY 3.2 22.8 + - - +
96A THR 2.9 19.3 + - - +
97A LEU 3.9 3.1 - - - +
99A GLU* 1.3 76.1 - - - +
101A LEU* 1.3 57.6 + - - +
103A TRP* 3.3 5.0 + - - +
104A ALA* 3.0 28.2 + - - +
183A LEU* 2.9 43.2 + - + +
184A SER 4.0 1.2 - - - -
185A LEU* 2.6 34.7 + - - +
952A 1PE 4.3 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 2.9 38.1 + - + +
98A ASP* 3.7 7.6 - - - +
99A GLU 3.2 0.2 - - - -
100A LYS* 1.3 75.0 - - - +
102A ARG* 1.3 60.6 + - - +
104A ALA* 4.3 2.5 - - - -
105A PHE* 2.9 25.6 + - - +
166A LEU* 4.8 1.5 - - - +
169A PHE* 3.4 22.3 - - + -
170A GLN* 4.2 24.2 - - + +
173A SER* 3.5 28.5 - - - +
174A LYS* 4.1 28.9 - - + -
183A LEU* 3.3 24.7 - - + -
951A 1PE 4.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASP* 3.2 45.8 + - - +
99A GLU* 3.3 23.9 + - - +
101A LEU* 1.3 77.0 - - - +
103A TRP* 1.3 62.4 + - - +
105A PHE* 3.4 7.6 + - - +
106A LYS* 3.2 41.4 + - - +
166A LEU* 4.5 18.4 - - + -
170A GLN* 3.7 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 4.2 10.3 - - + -
71A VAL* 2.9 49.0 + - + +
72A PHE* 3.8 19.3 - + - -
88A ALA* 4.3 13.5 - - - +
91A VAL* 4.0 27.8 - - + -
92A THR* 3.6 28.5 - - + +
99A GLU 3.2 12.2 + - - +
100A LYS* 3.5 8.7 - - - +
102A ARG* 1.3 76.4 - - - +
104A ALA* 1.3 64.5 + - - +
106A LYS* 3.2 20.1 + - - +
107A LEU* 3.0 35.8 + - + +
952A 1PE 3.5 29.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS 3.0 16.8 + - - +
101A LEU* 3.7 6.3 - - - +
102A ARG 3.4 0.2 - - - -
103A TRP* 1.3 73.5 - - - +
105A PHE* 1.3 67.2 + - - +
107A LEU* 3.1 7.6 + - - +
108A TYR* 3.0 32.3 + - + -
169A PHE* 3.9 17.0 - - + -
183A LEU* 5.0 1.8 - - + -
951A 1PE 4.5 9.4 - - - -
952A 1PE 3.8 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU 2.9 18.1 + - - +
102A ARG 3.6 6.5 - - - +
104A ALA* 1.3 78.3 - - - +
106A LYS* 1.3 60.9 + - + +
108A TYR* 3.2 2.1 + - - +
109A ASP* 2.8 46.4 + - + +
114A GLY* 3.5 38.6 - - - -
115A TYR* 4.1 2.9 - - - -
116A ILE* 3.4 29.4 - - + -
164A LEU 3.8 4.9 - - - -
165A THR 3.7 7.0 - - - -
166A LEU* 3.4 48.7 - - + -
169A PHE* 3.8 19.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 4.1 18.7 - - + +
102A ARG* 3.2 28.7 + - - +
103A TRP* 3.2 23.5 + - - +
105A PHE* 1.3 84.0 - - + +
107A LEU* 1.3 63.1 + - - +
109A ASP* 3.7 18.0 - - - +
110A LEU* 5.3 0.2 - - - -
112A ASN* 5.6 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 4.3 19.1 - - + -
67A PHE* 3.5 39.9 - - + +
68A VAL* 4.1 12.1 - - + +
71A VAL* 4.5 11.4 - - + +
103A TRP* 3.0 24.4 + - + +
104A ALA* 3.1 9.8 + - - +
106A LYS* 1.3 80.1 - - - +
108A TYR* 1.3 68.3 + - + +
110A LEU* 3.5 19.1 - - - +
124A ILE* 3.7 10.5 - - + +
952A 1PE 3.7 32.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA* 3.0 31.3 + - + +
105A PHE 4.0 0.2 - - - +
107A LEU* 1.3 79.6 - - + +
109A ASP* 1.3 60.6 + - - +
110A LEU* 2.9 12.3 + - - +
116A ILE* 3.5 27.5 - - + +
120A GLU* 3.4 22.3 - - - +
121A MET* 4.0 30.7 - - + -
124A ILE* 3.4 38.8 - - + -
125A VAL* 4.5 3.1 - - + -
128A ILE* 4.0 5.9 - - - +
169A PHE* 4.3 11.7 - + - -
951A 1PE 3.5 44.7 + - - -
952A 1PE 4.0 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 2.8 34.9 + - + +
106A LYS* 3.7 13.6 - - - +
107A LEU 3.4 0.6 - - - -
108A TYR* 1.3 69.6 - - - +
110A LEU* 1.3 65.0 + - - +
111A ASP* 3.1 6.9 - - - +
112A ASN* 3.0 20.1 + - - +
113A ASP* 3.1 4.3 + - - +
114A GLY* 2.8 28.5 + - - -
115A TYR 3.5 10.3 - - - +
116A ILE* 4.0 4.2 - - + +
120A GLU* 4.0 4.5 - - - -
1598A CA 2.2 31.2 - - - -
----------------------------------------------------------
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