Contacts of the helix formed by residues 115 - 130 (chain A) in PDB entry 5U03
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 PRO 115 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLN* 4.9 3.4 - - + +
113A VAL 3.4 4.5 - - - -
114A VAL* 1.3 88.4 - - + +
116A HIS* 1.3 82.7 + - + +
118A THR* 2.9 18.1 + - - +
119A ASP* 2.9 36.8 + - - +
232D MET* 4.2 36.8 - - + -
233D PHE* 5.3 2.5 - - + -
235D HIS* 6.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A VAL* 5.9 1.1 - - + +
106A TYR* 3.9 27.7 + + + +
109A LYS* 6.3 0.2 - - - +
110A THR 3.8 9.5 + - - -
111A VAL* 3.6 33.3 - - + +
112A GLN* 2.9 39.1 + - + +
115A PRO* 1.3 99.6 - - + +
117A ILE* 1.3 59.1 + - + +
119A ASP* 3.4 7.6 + - - +
120A ALA* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 4.5 15.9 - - + -
94A TYR* 6.1 6.1 - - + -
97A VAL* 3.9 35.7 - - + -
111A VAL* 4.9 7.9 - - + -
112A GLN 3.1 4.5 + - - +
113A VAL* 2.8 37.5 + - + +
116A HIS* 1.3 71.0 - - + +
118A THR* 1.3 56.3 + - - +
120A ALA* 2.9 5.6 + - - +
121A ILE* 2.7 49.4 + - + +
158A PRO* 4.8 10.1 - - + -
43C ILE* 5.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 2.9 23.6 + - + +
114A VAL* 3.8 10.4 - - + +
115A PRO* 2.9 22.2 + - - +
117A ILE* 1.3 76.1 - - - +
119A ASP* 1.3 60.3 + - - +
121A ILE* 3.4 11.4 + - + +
122A GLN* 3.1 34.1 + - - +
158A PRO 3.5 23.1 - - - +
161A GLU* 3.8 22.9 - - + +
162A ALA* 3.8 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PRO* 2.9 40.4 + - - +
116A HIS* 3.6 8.1 - - - +
117A ILE 3.1 0.2 - - - -
118A THR* 1.3 78.1 + - - +
120A ALA* 1.3 60.1 + - - +
122A GLN* 3.0 18.8 + - - +
123A GLU* 2.8 40.3 + - + +
169A LYS* 4.1 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 5.1 4.3 - - + -
96A TYR* 5.2 5.6 - - + -
97A VAL* 4.6 18.6 - - + -
106A TYR* 5.7 4.3 - - - +
116A HIS 3.0 13.6 + - - +
117A ILE* 2.9 12.8 + - - +
119A ASP* 1.3 74.6 - - - +
121A ILE* 1.3 58.4 + - - +
123A GLU* 3.0 20.2 + - - +
124A TRP* 2.8 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 5.4 2.2 - - + -
93A ILE* 4.4 9.0 - - + -
117A ILE* 2.7 32.6 + - + +
118A THR* 3.5 11.4 - - - +
119A ASP 3.1 0.2 - - - -
120A ALA* 1.3 75.1 - - + +
122A GLN* 1.3 64.2 + - + +
124A TRP* 3.0 12.7 + - + +
125A VAL* 3.0 28.7 + - + +
158A PRO* 3.7 28.3 - - + +
159A PHE* 3.6 44.4 - - + -
162A ALA* 3.6 14.1 - - + -
163A PHE* 5.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 3.1 20.6 + - - +
119A ASP* 3.0 14.3 + - - +
121A ILE* 1.3 74.7 - - - +
123A GLU* 1.3 62.2 + - - +
125A VAL* 3.2 13.5 + - + +
126A MET* 3.2 24.3 + - - +
162A ALA* 3.0 33.1 + - + +
165A GLN* 4.0 9.3 - - - +
166A PHE* 3.5 38.0 - - + +
169A LYS* 2.7 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 4.8 1.9 + - - -
100A LYS* 5.9 2.3 - - - -
119A ASP* 2.8 24.1 + - + +
120A ALA* 3.2 19.1 - - - +
122A GLN* 1.3 76.5 - - - +
124A TRP* 1.3 52.4 + - - +
126A MET* 2.9 10.8 + - - +
127A ARG* 2.7 67.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASP* 5.8 3.6 - - - -
88A LEU* 3.6 29.6 - - + -
92A LYS* 3.7 34.1 - - + -
93A ILE* 4.0 25.6 - - + +
96A TYR* 3.8 48.4 - + + -
120A ALA* 2.8 36.1 + - + +
121A ILE* 3.0 12.3 + - - +
123A GLU* 1.3 74.9 - - - +
125A VAL* 1.3 65.0 + - + +
127A ARG* 2.8 43.3 + - - +
128A GLN* 2.6 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 3.4 33.9 - - + -
37A ILE* 4.0 15.6 - - + +
39A ILE* 5.6 4.3 - - + -
121A ILE* 3.0 23.6 + - + +
122A GLN* 3.2 15.3 - - + +
123A GLU 3.1 0.2 - - - -
124A TRP* 1.3 76.1 - - + +
126A MET* 1.3 50.6 + - - +
128A GLN* 3.4 0.9 + - - -
129A ALA* 2.7 34.8 + - - +
145A ILE* 4.7 9.4 - - + -
163A PHE* 4.3 24.5 - - + -
166A PHE* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 3.1 29.8 - - - +
122A GLN 3.2 11.0 + - - +
123A GLU* 2.9 10.3 + - - +
125A VAL* 1.3 76.6 - - + +
127A ARG* 1.4 66.5 + - - +
129A ALA* 3.7 4.9 - - + -
130A LEU* 3.0 57.3 + - + +
139A GLU* 4.6 4.9 - - - +
166A PHE* 4.8 10.5 - - + -
170A VAL* 6.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 2.9 33.0 + - - -
100A LYS* 6.1 0.2 - - - +
120A ALA 3.6 2.2 + - - -
123A GLU* 2.7 52.2 + - + +
124A TRP* 2.8 67.4 + - - +
126A MET* 1.4 73.8 - - - +
128A GLN* 1.3 70.3 + - - +
130A LEU* 4.0 8.6 + - - +
131A ILE* 3.3 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 4.9 7.3 + - - +
37A ILE* 3.6 27.6 - - + +
85A ASP* 3.1 49.9 + - + +
86A ASN* 4.3 11.8 + - - +
88A LEU* 3.5 18.4 - - - +
124A TRP* 2.6 40.0 + - - +
127A ARG* 1.3 96.2 + - - +
129A ALA* 1.3 67.2 + - - +
130A LEU 3.1 1.8 - - - -
131A ILE* 3.0 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.0 34.3 - - + +
3A TYR* 3.8 26.2 - - + +
35A THR* 5.4 2.5 - - - -
37A ILE* 4.7 3.1 - - + +
125A VAL 2.7 20.0 + - - +
126A MET* 3.1 16.8 + - + +
128A GLN* 1.3 78.2 - - - +
130A LEU* 1.3 59.6 + - - +
131A ILE 3.1 1.6 + - - -
139A GLU* 3.3 9.5 - - - +
140A PRO* 3.3 5.2 - - - +
143A CYS* 5.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A MET* 3.0 40.5 + - + +
127A ARG* 4.2 7.0 - - - +
128A GLN 3.1 0.2 - - - -
129A ALA* 1.3 77.2 - - - +
131A ILE* 1.4 58.7 + - + +
132A PRO* 3.4 10.2 - - - +
139A GLU* 3.7 36.0 + - + +
140A PRO* 4.7 2.0 - - - -
----------------------------------------------------------
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