Contacts of the helix formed by residues 87 - 96 (chain B) 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 87 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LYS* 3.4 25.4 - - - +
109A GLU* 3.0 19.8 + - + +
85B ALA 3.4 2.8 + - - -
86B LYS* 1.3 71.3 - - - +
88B ALA* 1.3 62.1 + - - +
89B ALA* 2.9 5.8 - - + +
90B VAL* 2.9 15.5 + - + +
91B GLN* 2.8 15.3 - - - +
104B CYS 4.5 0.9 - - - +
105B PHE* 3.7 21.8 - - - +
106B GLU* 3.5 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 4.1 18.8 - - + -
52B VAL* 4.1 19.5 - - + +
76B VAL* 4.1 15.7 - - + -
82B VAL* 5.5 2.7 - - + -
86B LYS 3.5 1.4 + - - -
87B ALA* 1.3 71.6 - - - +
89B ALA* 1.3 62.4 + - - +
90B VAL 3.1 0.7 + - - -
91B GLN* 3.3 17.3 + - - +
92B ILE* 3.1 26.8 + - + +
106B GLU* 2.7 20.0 + - - +
138B THR* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 3.4 31.9 - - + +
76B VAL* 3.5 22.0 - - + +
87B ALA* 2.9 1.4 - - + +
88B ALA* 1.3 79.8 - - - +
90B VAL* 1.3 56.7 + - - +
92B ILE* 3.9 2.0 - - - +
93B HIS* 2.9 31.2 + - - +
104B CYS* 3.9 4.4 - - + -
105B PHE* 3.5 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 4.0 15.9 - - - +
179A THR* 4.1 10.7 - - + +
181A ASP* 4.0 15.9 - - - -
308A GLY 3.4 30.1 - - - +
310A VAL* 3.9 26.9 - - + -
86B LYS* 4.0 7.9 - - + -
87B ALA* 2.9 16.9 + - + +
89B ALA* 1.3 75.6 - - - +
91B GLN* 1.3 68.4 + - - +
93B HIS* 3.3 7.0 + - - +
94B ASN* 3.1 20.6 + - - +
104B CYS* 4.1 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ASP* 3.5 17.7 - - - +
183A TYR* 4.0 20.1 + - - +
52B VAL* 3.9 33.8 - - + +
82B VAL* 4.8 10.1 - - - +
83B ASP* 5.8 2.0 - - - +
86B LYS* 3.7 24.0 + - - +
87B ALA 2.8 27.4 + - - +
88B ALA* 3.3 11.5 + - - +
90B VAL* 1.3 73.6 - - - +
92B ILE* 1.3 58.4 + - - +
94B ASN* 3.2 3.3 + - - +
95B LEU* 2.8 35.1 + - + +
382B ARG* 6.3 1.2 - - - +
384B TYR* 5.0 12.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE 4.5 1.8 - - - +
52B VAL* 3.8 36.8 - - + +
55B GLY* 4.2 10.3 - - - -
56B ALA* 4.4 7.2 - - + +
74B VAL* 4.8 5.6 - - + -
76B VAL* 3.9 25.1 - - + -
88B ALA* 3.1 15.9 + - + +
89B ALA* 4.0 5.2 - - - +
91B GLN* 1.3 73.2 - - - +
93B HIS* 1.3 66.9 + - - +
95B LEU* 3.3 6.2 + - - +
96B LEU* 2.9 47.9 + - + +
136B ILE* 3.6 26.0 - - + -
138B THR* 5.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A THR* 3.9 28.4 - - + +
74B VAL* 4.1 10.9 - - + +
89B ALA 2.9 19.3 + - - +
90B VAL* 3.6 3.6 + - - +
92B ILE* 1.3 76.1 - - - +
94B ASN* 1.3 65.5 + - - +
96B LEU 4.0 0.2 - - - -
97B GLY* 3.3 15.8 + - - -
98B ILE* 3.3 58.8 + - + +
99B GLN 2.8 24.2 + - - -
100B PRO* 4.1 9.3 - - + +
102B ALA* 4.2 7.9 - - + +
104B CYS* 3.5 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ASP* 3.2 38.8 + - + +
90B VAL 3.1 8.8 + - - +
91B GLN 3.4 7.5 + - - +
92B ILE 3.1 0.2 - - - -
93B HIS* 1.3 80.5 + - - +
95B LEU* 1.3 67.7 + - - +
97B GLY* 3.1 14.7 + - - -
386B ARG* 4.0 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 3.8 29.4 - - + +
56B ALA* 4.2 14.4 - - + -
91B GLN* 2.8 23.9 + - + +
92B ILE* 3.3 4.7 + - - +
94B ASN* 1.3 76.5 - - - +
96B LEU* 1.3 61.2 + - - +
97B GLY 3.5 0.3 + - - -
372B PHE* 3.5 46.3 - - + -
384B TYR* 4.2 23.6 - - + -
386B ARG* 3.4 44.6 + - - +
390B GLU* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 3.9 22.0 - - + +
59B ALA* 3.8 9.6 - - + -
60B LYS* 4.1 11.9 - - + -
63B ILE* 3.5 27.5 - - + +
68B LYS* 3.3 27.6 + - - +
92B ILE* 2.9 41.1 + - + +
95B LEU* 1.3 78.8 - - + +
97B GLY* 1.3 63.0 + - - +
98B ILE* 3.4 12.7 + - + -
134B LEU* 3.7 25.1 - - + -
372B PHE* 4.4 9.4 - - + -
----------------------------------------------------------
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