Contacts of the strand formed by residues 59 - 72 (chain A) in PDB entry 6IY6
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 VAL 59 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 1.3 71.1 - - - +
60A VAL* 1.3 62.1 + - - +
61A TRP* 5.8 2.6 - - + -
117A GLU* 4.0 23.8 - - + +
118A GLY 3.6 4.7 - - - +
119A VAL* 4.2 15.5 - - + -
140A GLN* 3.9 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL 5.5 0.2 - - - -
46A VAL* 4.0 25.8 - - + -
51A LEU* 3.8 23.3 - - + -
55A LYS* 4.7 11.0 - - + -
58A GLU* 4.1 24.9 - - + +
59A VAL* 1.3 76.8 - - - +
61A TRP* 1.3 63.0 + - - +
62A VAL* 4.4 4.0 - - + +
116A VAL 3.8 0.7 - - - +
117A GLU* 3.6 3.1 - - - +
118A GLY 3.0 33.8 + - - +
120A VAL* 3.8 16.6 - - + -
137A LEU* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 3.5 56.1 - - + +
44A VAL 3.6 18.1 + - - +
45A LEU* 3.7 13.9 - - + -
46A VAL* 2.9 28.7 + - - +
59A VAL* 5.8 2.9 - - + -
60A VAL* 1.3 74.5 - - - +
62A VAL* 1.3 63.9 + - - +
115A ASP* 4.0 21.5 - - + -
116A VAL 3.2 10.8 - - - -
117A GLU* 3.5 61.2 + - + -
141A LYS* 4.2 19.5 - - + -
143A TYR* 4.4 12.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.6 3.3 - - - +
46A VAL* 3.8 26.7 - - + +
48A VAL* 4.1 18.4 - - + -
51A LEU* 3.9 21.8 - - + -
60A VAL* 4.4 7.4 - - + -
61A TRP* 1.3 78.6 - - - +
63A ARG* 1.3 62.0 + - - +
64A ALA* 4.1 21.1 - - + -
80A LEU* 4.8 9.2 - - + -
82A GLN* 5.4 0.4 - - - +
114A VAL 3.5 2.4 - - - +
115A ASP* 3.5 1.1 - - - -
116A VAL* 2.7 49.7 + - + +
137A LEU* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.5 13.5 - - - +
45A LEU* 3.8 28.0 - - + +
46A VAL 4.9 1.7 + - - +
62A VAL* 1.3 72.7 - - - +
64A ALA* 1.3 61.4 + - - +
82A GLN* 4.2 20.6 + - - +
113A ILE* 3.7 24.0 - - + -
114A VAL 3.3 4.3 - - - +
115A ASP* 2.7 40.2 + - - +
145A ILE* 4.3 4.0 - - - +
295B PHE 3.4 8.1 + - - -
296B ASN* 2.6 33.6 + - - +
297B TYR* 3.2 18.8 - - - -
464B PRO* 6.0 2.7 - - - -
465B PRO* 3.4 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 4.4 5.4 - - + -
62A VAL* 3.9 13.3 - - + -
63A ARG* 1.3 73.1 - - - +
65A ARG* 1.3 60.6 + - - +
80A LEU* 3.8 29.4 - - + -
81A ARG 3.3 17.7 - - - +
82A GLN* 4.6 2.2 - - + -
113A ILE* 3.4 5.5 - - - +
114A VAL* 2.8 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA* 1.3 72.4 - - - +
66A VAL* 1.3 62.2 + - - +
67A HIS 3.5 1.3 + - - -
80A LEU* 3.3 7.9 - - - -
81A ARG* 2.9 66.0 + - - +
82A GLN* 6.2 0.7 - - - +
111A GLU* 3.4 20.6 + - - +
112A SER 3.4 5.8 - - - -
113A ILE* 3.8 20.7 - - + +
188A ARG* 2.9 32.8 - - - +
258B ILE 4.9 0.4 + - - -
259B CYS 3.4 4.6 + - - -
261B ASP* 2.7 40.5 + - - +
462B GLY* 1.9 40.6 + - - -
464B PRO* 4.7 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 1.3 71.1 - - - +
67A HIS* 1.3 61.6 + - - +
68A THR* 4.3 7.6 - - - +
69A SER* 3.8 29.8 - - - +
78A LEU* 4.0 22.2 - - + -
79A VAL 4.0 2.7 - - - +
80A LEU* 4.6 3.6 - - + -
108A ILE* 3.7 30.5 - - + +
109A ASN 4.5 5.4 - - - +
110A LYS* 3.9 4.5 - - + -
111A GLU* 3.0 25.7 + - - -
112A SER 3.1 17.9 + - - +
114A VAL* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG 3.5 2.0 + - - -
66A VAL* 1.3 74.3 - - - +
68A THR* 1.3 75.1 + - - +
79A VAL* 2.8 41.5 + - + +
81A ARG* 3.4 28.5 + - + +
86A ASN* 4.8 8.2 + - - -
110A LYS* 4.4 9.5 - - - +
111A GLU* 4.3 9.8 - - - +
604A PO4 3.6 21.9 + - - -
605A PO4 3.2 41.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 4.3 4.2 - - - +
67A HIS* 1.3 88.8 + - - +
69A SER* 1.3 61.8 + - - +
70A ARG* 4.1 22.8 + - + +
77A PHE 4.3 0.2 - - - +
78A LEU* 3.5 1.7 - - - +
79A VAL* 2.8 38.4 + - - +
110A LYS* 4.9 8.1 - - - +
604A PO4 2.9 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 3.8 18.0 - - - +
68A THR* 1.3 76.6 - - - +
70A ARG* 1.3 61.9 + - - +
71A ALA* 4.0 0.9 + - - +
76A CYS* 4.9 1.3 - - - -
77A PHE 3.4 10.3 - - - -
78A LEU* 4.2 12.8 - - - +
105A ALA 4.4 7.2 - - - -
106A ALA* 3.8 24.5 + - - +
108A ILE 4.1 8.8 + - - -
110A LYS* 5.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 4.1 18.5 - - + +
69A SER* 1.3 71.9 - - - +
71A ALA* 1.3 55.0 + - - +
76A CYS* 4.1 0.2 - - - -
77A PHE* 2.8 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER 4.0 1.2 + - - -
70A ARG* 1.3 74.3 - - - +
72A LYS* 1.3 61.5 + - - +
73A GLY 4.3 0.9 - - - +
75A GLN 3.6 13.0 - - - +
76A CYS* 3.9 8.1 - - + -
102A VAL* 5.4 2.2 - - + +
106A ALA* 3.6 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 1.3 72.9 - - - +
73A GLY* 1.3 65.2 + - - +
74A LYS 3.1 4.0 + - - -
75A GLN* 3.0 20.9 + - + +
----------------------------------------------------------
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