Contacts of the helix formed by residues 101 - 118 (chain A) in PDB entry 2PKG
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 GLU 101 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASP* 3.4 40.8 + - + +
99A VAL* 3.5 3.4 - - - +
100A GLU* 1.3 76.5 - - - +
102A THR* 1.3 70.5 + - - +
103A VAL* 3.2 29.9 - - + +
104A VAL* 3.1 21.2 + - + +
105A ARG* 3.5 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU 3.1 3.4 + - - +
101A GLU* 1.3 73.0 + - - +
103A VAL* 1.3 82.3 + - - +
104A VAL 2.7 1.2 + - - -
105A ARG* 2.8 40.5 + - - +
106A ASP* 2.6 41.0 + - - +
146C MET* 6.3 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.8 31.2 - - + +
101A GLU* 3.2 21.1 + - + +
102A THR* 1.3 79.0 + - - +
104A VAL* 1.3 65.8 + - + +
106A ASP* 3.2 18.7 - - - +
107A LYS* 3.5 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASP* 3.2 46.9 - - + +
66A LEU* 3.8 11.4 - - + +
67A LEU* 4.1 10.8 - - + +
70A ALA* 4.8 1.8 - - + +
96A LEU* 3.8 22.4 - - + +
99A VAL* 3.7 28.7 - - + -
101A GLU* 3.1 12.2 + - + +
102A THR 2.7 4.0 + - - -
103A VAL* 1.3 74.1 - - + +
105A ARG* 1.3 57.3 + - - +
106A ASP 2.7 14.3 + - - -
107A LYS* 2.8 18.7 + - - +
108A ALA* 3.2 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU 3.6 21.3 - - - +
97A ALA* 3.6 12.6 - - - +
98A THR 4.2 0.2 - - - +
99A VAL 3.1 20.5 + - - +
100A GLU 2.4 31.9 + - - -
101A GLU 3.5 0.8 + - - -
102A THR* 2.8 41.4 + - - +
104A VAL* 1.3 76.8 - - - +
106A ASP* 1.3 65.8 + - - +
108A ALA* 3.9 3.4 - - - -
109A VAL* 2.9 30.4 + - - +
141A PHE* 4.6 10.7 - - - -
142A THR* 3.6 26.4 - - - +
145A THR* 4.1 18.4 - - - +
146A SER* 3.1 23.5 + - - +
146C MET* 5.8 3.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A THR* 2.6 50.9 + - - +
103A VAL* 3.2 12.4 + - - +
104A VAL 2.7 0.8 + - - -
105A ARG* 1.3 77.9 + - - +
107A LYS* 1.3 63.1 + - - +
109A VAL* 3.3 4.6 + - - +
110A GLU* 3.1 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.2 34.1 - - + +
70A ALA* 4.1 11.0 - - + +
71A GLU* 4.2 33.7 - - + -
103A VAL 3.5 1.1 + - - +
104A VAL 2.8 13.6 + - - +
106A ASP* 1.3 71.3 - - - +
108A ALA* 1.3 58.9 + - - +
110A GLU* 2.4 71.3 + - - +
111A SER* 2.8 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 3.9 12.4 - - + +
93A LEU* 3.8 8.9 - - + +
96A LEU* 3.8 16.6 - - + -
97A ALA* 3.6 35.7 - - + +
104A VAL 3.2 3.1 + - - +
105A ARG* 3.9 6.7 - - - +
107A LYS* 1.3 77.9 - - - +
109A VAL* 1.3 58.3 + - - +
111A SER* 3.1 7.1 + - - -
112A LEU* 2.7 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA* 4.0 9.2 - - + -
105A ARG 2.9 19.8 + - - +
106A ASP* 3.7 4.5 - - - +
108A ALA* 1.3 76.4 - - - +
110A GLU* 1.3 58.8 + - - +
112A LEU* 4.0 7.2 - - + -
113A ARG* 2.8 40.2 + - + +
146A SER* 3.2 47.8 - - - +
149A GLY* 4.2 9.4 - - - +
150A LEU* 3.6 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASP 3.1 9.7 + - - +
107A LYS* 2.4 74.1 + - - +
109A VAL* 1.3 74.7 - - - +
111A SER* 1.3 55.4 + - - +
113A ARG* 3.4 10.7 + - - +
114A ALA* 3.0 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA 2.6 28.4 + - - -
71A GLU* 4.2 2.1 + - - -
73A LEU 4.3 4.5 - - - -
74A GLY* 3.6 20.7 - - - -
93A LEU* 4.0 14.4 - - - -
107A LYS* 2.8 14.7 + - - +
108A ALA* 3.4 8.5 - - - -
110A GLU* 1.3 70.9 + - - +
112A LEU* 1.3 69.4 + - - +
114A ALA* 2.8 19.0 + - - +
115A ILE* 2.9 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 4.4 10.8 - - + -
93A LEU* 3.5 33.7 - - + +
94A GLU 5.2 0.7 - - - +
97A ALA* 4.3 17.7 - - + -
108A ALA 2.7 15.8 + - - +
109A VAL* 3.6 15.0 - - + +
111A SER* 1.3 74.1 - - - +
113A ARG* 1.3 64.0 + - - +
115A ILE* 3.3 5.8 - - - +
116A SER* 3.0 21.3 + - - -
128A PHE* 3.8 22.1 - - + -
131A LEU* 4.3 20.0 - - + -
135A LEU* 4.4 7.2 - - + -
150A LEU* 3.3 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL* 2.8 31.1 + - - +
110A GLU* 3.4 8.5 - - - +
112A LEU* 1.3 78.6 - - - +
114A ALA* 1.3 57.1 + - - +
116A SER* 2.5 28.9 + - - -
117A HIS* 3.0 13.8 + - + -
149A GLY* 3.3 29.1 + - - +
150A LEU* 3.6 8.3 - - + -
152A SER* 5.0 3.6 - - - -
153A VAL* 4.5 18.5 - - + +
188A LYS* 4.9 8.7 - - - +
191A GLU* 3.3 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLY* 5.5 5.6 - - - +
110A GLU* 3.0 13.4 + - + +
111A SER* 2.8 19.1 + - - +
113A ARG* 1.3 67.6 - - - +
115A ILE* 1.3 61.7 + - + +
116A SER 2.9 9.4 + - - -
117A HIS* 3.3 24.4 + - - +
118A GLU* 4.1 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU 4.3 8.3 - - - +
74A GLY 3.7 20.6 - - - +
77A THR* 3.4 32.5 - - + -
86A VAL* 3.6 6.6 - - + +
89A LEU* 3.9 28.3 - - + -
90A LEU* 3.8 26.0 - - + -
93A LEU* 4.4 14.6 - - + -
111A SER 2.9 13.7 + - - +
112A LEU* 3.3 13.2 - - - +
114A ALA* 1.3 70.1 - - + +
116A SER* 1.3 65.6 + - - +
117A HIS 3.3 0.2 - - - -
118A GLU* 3.2 14.7 + - - +
119A HIS* 3.1 17.0 - - - +
128A PHE* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU 3.0 4.7 + - - -
113A ARG* 2.5 24.1 + - - -
114A ALA 2.9 0.8 - - - -
115A ILE* 1.3 75.7 - - - +
117A HIS* 1.3 72.8 + - - +
119A HIS* 3.0 32.7 + - - +
124A LEU* 4.0 4.3 - - - +
128A PHE* 3.3 34.1 - - - -
153A VAL* 3.5 18.0 - - - +
154A CYS 5.4 0.4 - - - -
157A ARG* 3.5 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 3.0 23.2 + - + -
114A ALA* 3.3 11.8 + - - +
115A ILE 3.3 0.2 - - - -
116A SER* 1.3 87.6 + - - +
118A GLU* 1.3 62.1 + - + +
119A HIS 2.8 14.2 + - - +
153A VAL* 3.7 17.2 - - + +
157A ARG* 3.6 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR* 3.4 45.1 + - + +
83A PRO* 3.2 39.4 - - + +
86A VAL* 3.0 15.2 - - + +
114A ALA 4.7 3.1 - - - +
115A ILE* 3.2 12.5 + - - +
116A SER 3.1 1.0 - - - -
117A HIS* 1.3 76.9 - - + +
119A HIS* 1.3 58.8 + - - +
----------------------------------------------------------
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