Contacts of the helix formed by residues 99 - 112 (chain B) in PDB entry 2GTP
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 ALA 99 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASP* 3.0 17.3 + - - +
98B SER* 1.3 76.5 + - - +
100B ARG* 1.3 79.1 + - - +
101B ALA 3.1 0.8 + - - -
102B ASP* 3.4 20.5 + - - +
103B ASP* 3.8 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 3.7 22.7 - - + -
97B ASP* 3.0 38.0 + - - +
99B ALA* 1.3 94.2 + - - +
101B ALA* 1.3 58.1 + - - +
103B ASP* 2.9 32.9 + - - +
104B ALA* 2.8 29.6 + - - +
129B ARG* 3.5 45.0 + - - +
130B LEU* 3.8 7.4 - - + +
133B ASP* 3.8 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 4.1 19.9 - - + -
98B SER* 3.1 17.6 + - - +
100B ARG* 1.3 76.9 - - - +
102B ASP* 1.3 61.7 + - - +
104B ALA* 3.1 5.6 + - - +
105B ARG* 3.1 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B SER 4.6 0.2 + - - -
99B ALA* 3.4 11.9 + - - +
101B ALA* 1.3 79.1 - - - +
103B ASP* 1.3 64.7 + - - +
105B ARG* 2.9 38.3 + - - +
106B GLN* 3.0 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ALA 4.2 6.3 - - - +
100B ARG* 2.9 35.5 + - - +
102B ASP* 1.3 80.3 - - - +
104B ALA* 1.3 53.1 + - - +
106B GLN* 3.3 6.0 + - - +
107B LEU 2.7 30.0 + - - -
126B VAL* 3.2 17.4 - - + +
129B ARG* 2.8 49.2 + - - +
130B LEU* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 4.2 18.4 - - + -
95B PHE* 4.0 22.0 - - + -
100B ARG 2.8 12.3 + - - +
101B ALA* 3.1 8.5 + - - +
103B ASP* 1.3 74.3 - - - +
105B ARG* 1.3 65.2 + - - +
107B LEU* 3.3 8.0 + - - +
108B PHE* 3.1 30.3 + - + -
130B LEU* 4.1 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA* 3.1 27.3 + - - +
102B ASP* 2.9 46.0 + - - +
104B ALA* 1.3 73.9 - - - +
106B GLN* 1.3 67.5 + - - +
108B PHE* 3.0 10.4 + - - +
109B VAL* 3.0 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ASP* 3.0 26.0 + - - +
103B ASP* 3.4 9.0 - - - +
105B ARG* 1.3 79.6 - - - +
107B LEU* 1.3 57.4 + - - +
109B VAL* 3.1 15.3 + - - +
110B LEU* 2.8 62.3 + - + +
122B GLU* 3.9 19.3 + - - +
126B VAL* 4.2 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 5.3 3.4 - - + +
81B ILE* 3.8 20.2 - - + -
82B ILE* 3.8 23.1 - - + -
85B ILE* 3.2 32.1 - - + -
103B ASP 2.7 17.1 + - - +
104B ALA* 3.4 11.7 - - - +
106B GLN* 1.3 73.1 - - - +
108B PHE* 1.3 60.9 + - + +
110B LEU* 4.1 2.6 - - - +
111B ALA* 2.8 36.1 + - + +
123B LEU* 3.9 10.5 - - + -
126B VAL* 3.9 10.9 - - + +
127B ILE* 3.7 30.7 - - + -
130B LEU* 4.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE* 3.9 37.2 - - + -
85B ILE* 3.8 26.0 - - + -
86B ARG* 4.0 36.8 - - + -
104B ALA* 3.1 25.2 + - + -
105B ARG* 3.0 10.5 + - - +
107B LEU* 1.3 81.8 - - + +
109B VAL* 1.3 64.3 + - + +
111B ALA* 4.0 4.3 - - - +
112B GLY* 3.1 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 3.0 26.9 + - + +
106B GLN* 3.6 19.7 - - - +
108B PHE* 1.3 76.5 - - + +
110B LEU* 1.3 68.7 + - + +
112B GLY* 3.3 10.6 + - - -
113B ALA* 3.6 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLN* 2.8 51.8 + - + +
107B LEU 4.1 2.0 - - - +
109B VAL* 1.3 73.8 - - + +
111B ALA* 1.3 57.0 + - - +
112B GLY 3.0 1.1 - - - -
113B ALA* 2.7 38.4 + - + +
120B THR* 5.2 5.2 - - + +
122B GLU* 3.7 37.7 - - + +
123B LEU* 4.1 35.3 - - + +
126B VAL* 4.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 4.0 20.9 - - + -
82B ILE* 4.0 25.4 - - + -
107B LEU* 2.8 24.8 + - + +
108B PHE 4.0 3.8 - - - +
110B LEU* 1.3 72.1 - - - +
112B GLY* 1.3 62.7 + - - +
113B ALA 3.1 7.0 + - - -
114B ALA* 4.3 1.4 + - - -
123B LEU* 4.8 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE 3.1 14.7 + - - -
109B VAL* 3.6 7.6 - - - -
110B LEU 3.0 1.6 - - - -
111B ALA* 1.3 76.8 - - - +
113B ALA* 1.3 55.3 + - - +
114B ALA 4.0 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