Contacts of the helix formed by residues 113 - 126 (chain A) in PDB entry 1XPM
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 113 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA* 3.6 12.5 - - + +
78A THR 4.6 0.4 - - - +
107A MET* 3.4 37.3 - - + +
108A LYS* 4.0 1.6 - - - -
109A GLU* 3.6 17.4 + - - +
111A SCY 3.6 1.6 - - - -
112A TYR* 1.3 77.9 - - - +
114A ALA* 1.3 61.2 + - - +
115A THR 3.2 0.7 + - - -
116A PRO* 3.3 22.0 - - - +
117A ALA* 3.5 9.9 + - - +
278A THR* 4.1 9.4 - - + +
105B PHE* 5.9 0.4 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
77A ALA* 3.4 18.5 - - + +
112A TYR 3.0 4.0 + - - -
113A ALA* 1.3 75.9 - - - +
115A THR* 1.3 57.5 + - - +
117A ALA* 3.2 6.4 - - - +
118A ILE* 3.0 32.1 + - - +
135A VAL* 4.3 3.8 - - + +
137A ALA* 4.1 10.5 - - + -
160A MET* 4.6 6.5 - - + -
278A THR* 3.8 18.0 - - - +
282A TYR* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A TYR* 3.0 8.3 + - + -
114A ALA* 1.3 74.6 - - - +
116A PRO* 1.3 72.9 - - - +
117A ALA 3.0 1.3 + - - -
118A ILE* 3.3 2.9 + - - +
119A GLN* 3.0 28.4 + - + +
282A TYR* 2.7 23.2 + - - -
304A SER* 2.7 30.3 + - - -
312A GLU* 3.6 32.5 - - - +
314A TYR* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A MET* 4.0 7.6 - - - -
112A TYR* 3.2 42.8 - - + +
113A ALA* 3.3 15.7 - - - +
115A THR* 1.3 91.9 - - - +
117A ALA* 1.3 54.7 + - - +
119A GLN* 3.8 6.5 - - + -
120A LEU* 2.8 38.7 + - + +
103B ARG* 4.3 10.3 - - - +
105B PHE* 3.7 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 3.9 20.3 - - + +
77A ALA* 5.1 2.7 - - + -
107A MET* 3.6 20.1 - - - -
113A ALA 3.5 12.9 + - - +
114A ALA* 3.2 13.2 + - - +
115A THR 3.0 0.6 - - - -
116A PRO* 1.3 78.3 - - - +
118A ILE* 1.3 57.9 + - - +
121A ALA* 3.0 28.9 + - - +
135A VAL* 3.7 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.7 6.3 - - + -
114A ALA 3.0 14.8 + - - +
115A THR* 3.4 10.8 - - - +
117A ALA* 1.3 73.0 - - - +
119A GLN* 1.3 72.1 + - + +
121A ALA* 3.5 7.5 - - - +
122A LYS* 3.1 22.0 + - - +
135A VAL* 3.9 17.3 - - + -
160A MET* 3.7 26.5 - - + -
162A ILE* 4.0 19.7 - - + +
171A LEU* 4.0 24.2 - - + +
282A TYR* 3.6 16.6 - - + +
314A TYR* 3.6 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A THR* 3.0 23.3 + - + +
116A PRO 4.0 1.1 - - - +
118A ILE* 1.3 79.6 - - + +
120A LEU* 1.3 61.9 + - - +
122A LYS* 3.3 19.9 + - - +
123A ASP* 3.1 26.3 + - - +
171A LEU* 4.4 12.8 - - - +
172A ASN 4.7 8.4 + - - +
173A GLU* 5.5 1.4 - - - +
175A ALA* 4.3 6.5 - - - +
312A GLU* 3.6 7.4 + - - +
314A TYR* 3.3 46.1 - - - +
103B ARG* 3.3 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 5.1 0.4 - - - -
75A ILE* 5.8 0.7 - - + -
107A MET* 3.9 11.9 - - + -
116A PRO* 2.8 21.9 + - + +
117A ALA 4.3 1.1 - - - +
119A GLN* 1.3 73.7 - - - +
121A ALA* 1.3 59.1 + - - +
123A ASP* 3.2 19.5 + - + +
124A TYR* 2.9 29.5 + - - +
73B MET* 4.0 13.9 - - + -
75B ILE* 5.1 0.7 - - + -
103B ARG* 4.2 11.4 - - - +
105B PHE* 3.7 30.7 - - + -
107B MET* 4.7 1.3 - - + -
120B LEU* 4.0 38.6 - - + +
124B TYR* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 4.2 13.2 - - + +
117A ALA 3.0 19.9 + - - +
118A ILE* 3.5 10.3 - - - +
120A LEU* 1.3 75.8 - - - +
122A LYS* 1.3 64.1 + - - +
124A TYR* 3.2 4.0 + - - +
125A LEU* 3.1 28.6 + - - +
133A VAL* 3.6 32.7 - - + +
135A VAL* 4.5 0.4 - - + -
162A ILE* 4.1 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.6 40.7 - - + +
118A ILE 3.1 12.2 + - - +
119A GLN* 3.4 17.0 - - - +
121A ALA* 1.3 78.4 - - - +
123A ASP* 1.3 64.4 + - - +
125A LEU* 3.2 12.3 + - - +
126A ALA* 3.3 10.4 + - - +
162A ILE* 4.2 2.8 - - + +
171A LEU* 3.9 40.2 - - + +
172A ASN 5.2 0.7 - - - +
173A GLU* 3.6 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 3.1 16.0 + - - +
120A LEU* 3.2 25.2 + - + +
122A LYS* 1.3 78.3 - - - +
124A TYR* 1.3 61.4 - - - +
126A ALA* 3.3 20.9 + - - +
127A THR 4.9 0.2 + - - -
173A GLU* 4.2 16.1 - - - +
103B ARG* 4.8 1.4 + - - -
123B ASP* 3.7 34.3 - - + +
124B TYR* 3.6 21.6 - - - +
128B ARG* 4.5 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY* 4.1 10.6 + - - -
73A MET* 3.6 28.5 - - + -
103A ARG* 3.5 30.9 - - - +
120A LEU 2.9 13.4 + - - +
121A ALA 3.4 6.7 - - - +
123A ASP* 1.3 77.6 - - - +
125A LEU* 1.3 71.0 + - + +
126A ALA 3.4 0.9 + - - -
127A THR 4.1 1.9 + - - -
128A ARG* 2.8 65.3 + - - +
131A GLU* 2.7 31.4 + - - -
133A VAL* 3.7 21.3 - - + -
120B LEU* 3.9 4.9 - - + -
123B ASP* 3.6 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.2 8.7 - - + -
121A ALA 3.1 19.4 + - - +
122A LYS 3.2 5.1 + - - +
124A TYR* 1.3 86.6 - - + +
126A ALA* 1.3 62.7 + - - +
127A THR 3.1 3.8 - - - -
128A ARG* 2.9 13.6 + - + +
131A GLU* 3.4 40.8 - - + +
132A LYS 3.9 1.6 - - - +
133A VAL* 4.0 10.1 - - + -
162A ILE* 3.4 40.6 - - + +
163A ALA* 3.8 11.2 - - - +
164A HIS* 2.6 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.0 12.1 - - + -
122A LYS 3.3 8.3 + - - +
123A ASP* 3.4 17.0 - - - +
124A TYR 3.3 2.2 - - - -
125A LEU* 1.3 77.3 - - - +
127A THR* 1.3 65.6 + - + +
164A HIS* 4.2 5.4 - - - -
126B ALA* 6.1 5.4 - - + -
296C ALA* 4.2 1.7 - - - +
297C GLY* 3.8 16.8 + - - -
318C LEU 4.9 1.7 - - - +
320C GLU* 4.3 21.4 + - + +
----------------------------------------------------------
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