Contacts of the strand formed by residues 86 - 95 (chain A) in PDB entry 2PN2
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 ARG 86 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR* 5.9 1.6 - - - -
80A MSE 3.3 14.7 - - - +
81A ALA* 2.9 48.9 + - + +
82A ALA 3.1 17.0 + - - -
83A ASP 3.7 2.4 + - - -
84A PRO* 3.1 43.4 + - + +
85A ARG* 1.3 77.6 - - - +
87A VAL* 1.3 68.7 + - - +
88A SER* 5.6 2.4 - - - +
122A HIS* 6.2 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR* 4.0 25.8 - - + +
46A LEU* 4.3 18.6 - - + -
47A ALA* 5.6 2.5 - - + +
78A LYS* 4.9 6.5 - - + -
79A VAL 3.7 5.8 - - - +
80A MSE 3.8 16.8 - - + -
86A ARG* 1.3 84.3 + - - +
88A SER* 1.3 61.1 + - - +
89A GLU 3.6 21.8 - - - +
90A VAL* 3.7 19.3 - - + -
122A HIS* 5.6 0.3 - - - +
125A ILE* 3.3 32.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 2.9 33.6 + - - +
80A MSE 3.6 4.7 + - - -
81A ALA* 3.9 22.4 - - - +
86A ARG* 3.7 3.7 + - - +
87A VAL* 1.3 73.7 - - - +
89A GLU* 1.3 68.9 + - - +
124A ASP 3.9 4.4 - - - +
125A ILE* 3.3 10.9 - - - +
126A PHE* 3.0 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 3.5 1.9 - - - -
79A VAL* 2.9 44.0 + - + +
87A VAL* 3.6 2.5 - - - +
88A SER* 1.3 95.3 + - - +
90A VAL* 1.3 68.1 + - - +
91A HIS* 2.6 41.8 + - - +
125A ILE* 4.0 1.6 - - - -
126A PHE* 3.4 31.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 4.1 24.9 - - + +
50A LEU* 4.1 20.0 - - + -
76A VAL* 4.0 24.5 - - + -
77A THR 3.5 4.3 - - - +
78A LYS* 5.0 0.4 - - + -
87A VAL* 3.7 18.6 - - + -
89A GLU* 1.3 78.4 - - - +
91A HIS* 1.3 62.6 + - - +
92A ILE* 3.3 23.7 - - + +
121A ILE* 4.9 3.6 - - + -
125A ILE* 4.0 9.8 - - + +
126A PHE 2.9 8.3 + - - +
127A GLN* 3.6 1.1 - - - -
128A LYS 2.9 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU 3.4 1.6 - - - +
76A VAL* 3.4 5.5 - - - +
77A THR* 2.8 56.9 + - + +
79A VAL* 4.1 14.6 - - + -
89A GLU* 2.6 39.2 + - + +
90A VAL* 1.3 78.6 - - - +
92A ILE* 1.3 60.8 + - - +
93A ALA 4.1 0.4 - - - -
126A PHE* 4.6 1.7 - + - -
128A LYS* 3.3 44.4 + - + +
130A ILE* 6.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.1 14.4 - - + -
51A ALA* 4.1 24.7 - - + +
54A MSE 4.4 9.6 - - + -
74A ALA* 3.8 19.3 - - + -
75A GLU 3.4 4.3 - - - +
76A VAL* 4.9 2.7 - - + -
90A VAL* 3.3 38.4 - - + +
91A HIS* 1.3 74.8 - - - +
93A ALA* 1.3 58.6 + - - +
94A ILE* 3.8 25.7 + - + -
127A GLN 5.0 0.2 - - - -
128A LYS 2.8 14.7 + - - +
129A VAL* 3.3 20.2 - - + +
130A ILE* 3.0 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR* 3.7 1.4 + - - +
74A ALA* 3.3 2.9 - - - -
75A GLU* 2.9 52.1 + - + +
91A HIS 4.1 0.4 - - - -
92A ILE* 1.3 70.5 - - - +
94A ILE* 1.3 62.1 + - - +
95A THR* 3.9 2.6 + - - -
130A ILE* 3.4 16.4 - - + -
132A HIS* 3.4 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A MSE 4.9 9.0 - - + -
55A LEU* 4.2 11.2 - - + -
58A ILE* 4.0 24.0 - - + -
72A THR* 3.7 21.8 - - + -
73A THR 3.3 9.6 - - - +
74A ALA* 4.4 4.7 - - + -
92A ILE* 3.8 21.8 - - + -
93A ALA* 1.3 73.9 - - - +
95A THR* 1.3 57.2 + - - +
96A PHE* 3.7 21.3 - - + -
112A ALA* 5.2 0.9 - - + -
129A VAL* 4.0 20.4 - - + -
130A ILE 2.7 16.2 + - - +
131A ILE* 3.3 9.3 - - + +
132A HIS 2.7 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLY 4.5 0.9 - - - +
72A THR* 3.4 3.9 - - - -
73A THR* 2.8 48.3 + - - +
93A ALA* 3.9 3.1 + - - +
94A ILE* 1.3 72.3 - - - +
96A PHE* 1.3 71.6 + - - +
132A HIS* 3.5 34.9 + - + +
----------------------------------------------------------
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