Contacts of the helix formed by residues 85 - 95 (chain A) in PDB entry 1RP1
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 TRP 85 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 3.5 28.3 - - + -
74A ILE 4.8 1.6 - - - -
75A HIS* 3.9 17.3 - - - +
77A PHE 4.9 2.4 + - - -
78A ILE* 4.0 16.5 - - + +
82A GLU* 3.1 29.7 + - + +
83A GLU 3.3 1.4 - - - -
84A ASN* 1.3 78.1 - - - +
86A LEU* 1.3 78.4 + - + +
88A ASP* 3.2 11.8 + - - +
89A MET* 2.8 50.0 + - + +
149A ILE* 5.2 1.1 - - + -
151A HIS* 3.7 34.6 + - + -
175A LEU* 4.7 3.8 - - + -
267A TYR* 3.4 57.4 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 3.3 52.0 - - + +
75A HIS* 3.8 33.7 - - + +
78A ILE* 4.4 5.8 - - + -
83A GLU 3.9 15.7 - - - +
84A ASN 3.3 0.2 - - - -
85A TRP* 1.3 110.6 - - + +
87A LEU* 1.3 57.2 + - - +
89A MET 3.3 1.4 + - - -
90A CYS* 3.0 23.0 + - - -
103A CYS* 3.7 22.7 - - + -
104A VAL 4.3 4.3 - - - +
105A ASP* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 3.5 57.4 - - + +
46A PRO 3.7 13.2 - - - +
47A ASN 4.2 8.3 - - - +
84A ASN* 3.3 28.1 + - + +
86A LEU* 1.3 74.8 - - - +
88A ASP* 1.3 67.0 + - - +
89A MET 3.1 1.6 - - - -
90A CYS* 3.2 8.0 + - + +
91A LYS* 2.9 44.8 + - + +
103A CYS* 4.1 4.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASN* 2.8 31.2 + - - +
85A TRP* 3.2 13.3 + - - +
87A LEU* 1.3 78.4 - - - +
89A MET* 1.3 62.8 + - - +
91A LYS* 3.5 16.2 + - - +
92A ASN* 3.4 24.5 + - - +
271A SER* 4.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 3.9 17.5 - - + -
85A TRP* 2.8 38.1 + - + +
86A LEU 3.5 9.6 - - - +
88A ASP* 1.3 75.1 - - - +
90A CYS* 1.3 65.9 + - - +
92A ASN* 3.2 12.8 + - - +
93A MET* 3.2 26.2 + - + +
149A ILE* 4.4 8.5 - - - -
175A LEU* 4.3 3.6 - - + -
267A TYR* 3.5 30.5 - - + +
270A TYR* 3.8 28.0 - - + -
271A SER* 3.9 15.7 - - - +
274A ILE* 3.9 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 4.3 5.8 - - + -
73A ILE* 3.7 1.0 - - - +
86A LEU 3.0 11.3 + - - -
87A LEU* 3.2 12.3 + - + +
89A MET* 1.3 75.2 - - - +
91A LYS* 1.3 58.6 + - - +
93A MET* 2.8 24.7 + - - +
94A PHE* 3.0 27.4 + - + -
101A CYS* 2.0 56.3 - - + -
103A CYS* 3.6 30.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 3.2 30.9 + - + +
47A ASN* 3.5 23.4 + - - +
87A LEU* 2.9 42.0 + - + +
88A ASP* 3.6 15.4 + - - +
89A MET 3.2 0.2 - - - -
90A CYS* 1.3 76.6 - - - +
92A ASN* 1.3 62.1 + - - +
94A PHE* 3.4 22.8 + - + +
95A LYS* 3.5 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASP 3.4 10.5 + - - +
89A MET 3.2 9.3 + - - +
90A CYS 3.2 1.0 - - - -
91A LYS* 1.3 75.2 - - - +
93A MET* 1.3 65.0 + - - +
95A LYS* 3.2 40.9 + - - +
96A VAL 3.7 2.1 + - - -
271A SER* 3.1 38.0 + - - +
272A GLU* 5.0 1.4 - - - +
274A ILE* 3.6 11.5 - - + +
275A LEU* 3.6 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 3.7 24.0 - - + -
73A ILE* 3.8 26.0 - - + -
89A MET* 3.2 20.5 + - + +
90A CYS* 2.8 8.1 + - - +
92A ASN* 1.3 77.7 - - - +
94A PHE* 1.3 58.1 + - - +
96A VAL* 3.0 4.8 + - - +
97A GLU* 2.8 48.8 + - - +
99A VAL* 4.0 8.5 - - + -
101A CYS* 3.7 24.0 - - - -
149A ILE* 3.8 24.0 - - + -
270A TYR* 4.9 1.6 - - + -
274A ILE* 3.8 24.0 - - + -
309A HIS* 4.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 3.5 32.8 - - + -
42A THR* 3.5 15.7 - - - -
43A ASN* 3.3 38.3 + - + +
46A PRO* 3.7 40.6 - - + -
90A CYS* 3.0 31.3 + - + -
91A LYS* 3.6 15.3 - - + +
92A ASN 3.3 0.6 - - - -
93A MET* 1.3 78.6 - - - +
95A LYS* 1.3 58.9 + - - +
96A VAL 3.5 0.3 + - - -
97A GLU 3.5 7.4 + - - +
99A VAL* 3.8 20.9 - - + -
101A CYS* 4.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LYS* 3.5 15.3 - - - +
92A ASN* 3.5 33.1 + - - +
93A MET 3.1 0.8 - - - -
94A PHE* 1.3 77.7 - - + +
96A VAL* 1.3 63.2 + - + +
275A LEU* 3.9 25.4 - - + +
----------------------------------------------------------
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