Contacts of the helix formed by residues 87 - 99 (chain C) in PDB entry 1PY1
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 LYS 87 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASP* 3.1 22.2 + - - +
84C GLU* 3.9 28.9 - - - +
85C VAL 3.1 3.7 - - - +
86C GLY* 1.3 80.3 - - - +
88C PHE* 1.3 64.5 + - - +
89C ARG* 4.0 10.8 - - + +
90C PHE* 3.2 4.2 + - - +
91C LEU* 3.1 23.1 + - - +
131C LYS* 4.3 8.3 - - + +
3G ASP* 3.7 36.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C GLY 4.1 0.2 + - - -
87C LYS* 1.3 66.2 - - - +
89C ARG* 1.3 64.5 + - - +
90C PHE 3.0 2.7 - - - -
91C LEU* 3.8 15.3 - - + -
92C ASN* 2.9 40.1 + - - +
131C LYS* 3.5 49.8 - - + -
134C GLU* 3.9 22.0 - - - -
135C ALA* 4.4 2.7 - - + -
3G ASP* 3.0 18.1 + - - -
4G ILE* 3.3 27.8 - - - +
5G SEP 4.2 1.6 - - - +
6G LEU* 3.5 50.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ARG* 6.1 3.1 - - - +
84C GLU* 5.8 0.9 - - - +
87C LYS* 3.1 11.4 - - + +
88C PHE* 1.3 78.2 - - - +
90C PHE* 1.3 58.7 + - + +
92C ASN* 4.8 0.3 - - - +
93C GLU* 3.5 23.4 + - - +
106D ARG* 4.9 24.0 - - - +
3G ASP* 2.9 34.9 + - - +
4G ILE* 3.9 38.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C THR* 3.8 38.8 - - + -
51C LEU* 4.4 5.2 - - + -
52C ALA* 3.9 23.8 - - + -
55C ILE* 4.2 9.4 - - + -
70C LEU* 3.8 29.8 - - + -
84C GLU 3.7 17.3 - - - +
85C VAL* 3.6 37.7 - - + -
87C LYS 3.2 4.4 + - - +
88C PHE 3.0 0.2 - - - -
89C ARG* 1.3 78.3 - - + +
91C LEU* 1.3 59.0 + - - +
92C ASN 3.1 1.8 - - - -
93C GLU* 2.6 37.8 + - + +
94C LEU* 3.3 27.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C VAL* 3.4 17.9 - - + +
86C GLY 3.8 11.2 - - - +
87C LYS 3.1 18.6 + - - +
88C PHE* 4.0 12.8 - - + -
90C PHE* 1.3 78.1 - - + +
92C ASN* 1.3 63.0 + - - +
94C LEU* 3.1 17.0 + - + +
95C ILE* 3.0 25.0 + - + +
119C LEU* 4.1 26.5 - - + -
122C TRP* 5.2 0.7 - - + -
131C LYS* 3.7 35.4 - - + +
132C ILE* 3.8 14.1 - - + +
135C ALA* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C PHE* 2.9 24.8 + - - +
89C ARG 4.8 0.4 - - - +
90C PHE 2.8 2.0 + - - -
91C LEU* 1.3 75.1 - - - +
93C GLU* 1.3 71.5 + - - +
95C ILE* 2.9 8.3 + - - +
96C LYS* 2.8 32.0 + - - +
4G ILE* 3.3 20.0 - - + +
5G SEP 3.1 23.0 + - - -
6G LEU* 3.6 9.9 - - - +
7G LEU* 2.6 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA* 3.7 25.4 - - + -
56C GLN* 3.0 32.2 + - - +
89C ARG 3.5 17.5 - - - +
90C PHE* 2.6 20.3 + - + +
92C ASN* 1.3 78.0 - - - +
94C LEU* 1.3 60.1 + - + +
96C LYS* 3.4 32.9 + - - +
97C VAL* 3.3 25.1 + - - +
103D LEU* 6.0 2.1 - - - +
106D ARG* 5.2 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA* 6.4 0.4 - - - -
55C ILE* 4.0 37.9 - - + -
67C LEU* 4.5 4.0 - - + -
70C LEU* 4.3 8.3 - - + -
90C PHE* 3.3 31.1 + - + +
91C LEU* 3.1 17.6 + - + +
93C GLU* 1.3 77.4 - - + +
95C ILE* 1.3 63.9 + - + +
97C VAL* 3.1 15.7 + - - +
98C VAL* 3.3 17.2 + - - +
115C ILE* 4.2 26.9 - - + +
118C LEU* 6.3 0.9 - - + -
119C LEU* 3.9 28.7 - - + -
122C TRP* 4.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU 3.0 17.3 + - - +
92C ASN* 2.9 14.4 + - - +
94C LEU* 1.3 72.1 - - + +
96C LYS* 1.3 61.9 + - - +
98C VAL* 3.2 6.7 + - - -
99C SER* 2.7 44.3 + - - -
119C LEU* 5.8 3.8 - - + -
135C ALA* 4.3 14.6 - - + +
138C MET* 4.3 17.5 - - + -
139C LEU* 3.7 23.1 - - + -
6G LEU* 3.5 33.2 - - + -
7G LEU* 3.6 20.4 - - + -
8G LYS* 4.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLN* 5.2 4.7 - - - +
92C ASN* 2.8 22.2 + - - +
93C GLU* 3.4 40.1 + - - +
94C LEU 3.3 0.2 - - - -
95C ILE* 1.3 73.8 - - - +
97C VAL* 1.3 61.7 + - - +
99C SER 3.6 0.9 - - - +
102C TYR* 3.4 27.5 - - + +
103C LEU* 2.9 39.5 + - + +
104C GLY 3.4 2.1 + - - -
103D LEU* 6.3 1.2 - - - +
7G LEU* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ILE* 4.2 23.1 - - + +
56C GLN* 3.6 28.7 - - + -
93C GLU 3.3 16.2 - - - +
94C LEU* 3.1 8.2 + - - +
96C LYS* 1.3 77.2 - - - +
98C VAL* 1.3 57.3 + - + +
103C LEU* 4.2 10.5 - - + -
104C GLY* 3.4 7.6 - - - -
107C THR* 3.0 48.0 + - + +
111C VAL* 4.3 4.7 - - + -
115C ILE* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LEU 3.3 7.4 + - - +
95C ILE* 3.6 8.5 - - - +
97C VAL* 1.3 76.2 - - - +
99C SER* 1.3 68.6 + - - +
100C PRO* 3.3 10.0 - - - +
104C GLY* 3.7 1.7 - - - -
112C LYS* 3.4 58.2 - - + +
115C ILE* 3.8 24.7 - - + -
116C LEU* 4.6 4.5 - - + -
119C LEU* 5.6 0.2 - - + -
139C LEU* 3.8 35.4 - - + -
144C ILE* 4.4 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ILE* 2.7 34.7 + - - -
96C LYS 3.6 0.7 - - - +
97C VAL 3.7 0.2 - - - -
98C VAL* 1.3 73.1 - - - +
100C PRO* 1.3 64.9 - - - +
101C LYS* 3.5 14.7 + - - +
102C TYR* 2.9 35.6 + - - -
104C GLY* 2.8 19.0 + - - -
139C LEU* 5.2 0.9 - - - -
142C GLN* 3.9 17.2 + - - -
144C ILE* 4.5 3.4 - - - -
8G LYS* 4.5 1.6 + - - -
----------------------------------------------------------
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