Contacts of the strand formed by residues 56 - 64 (chain A) in PDB entry 6V65
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 56 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 4.2 21.8 - - + -
47A VAL 3.2 18.4 - - - +
48A PRO* 3.6 9.0 - - + -
49A HIS* 3.2 18.6 + - - -
54A GLY 4.1 5.4 - - - +
55A CYS* 1.3 77.6 - - - +
57A ASP* 1.3 66.3 + - - +
58A PHE* 3.9 18.7 - - + -
122A ASP 5.8 0.4 + - - -
123A ILE* 4.7 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 3.2 5.2 - - - +
47A VAL* 2.8 33.7 + - + +
49A HIS* 2.7 34.7 + - - -
56A ALA* 1.3 75.6 - - - +
58A PHE* 1.3 63.6 + - - +
59A PHE* 3.6 24.7 - - + -
75A MET* 3.3 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.9 19.7 - + - -
44A VAL* 6.1 0.2 - - + -
45A PHE 3.5 7.2 - - - +
46A LYS* 3.5 31.9 - - + -
56A ALA* 3.9 22.4 - - + -
57A ASP* 1.3 75.3 - - - +
59A PHE* 1.3 62.1 + - - +
75A MET* 3.3 9.1 - - - +
76A LEU* 2.8 54.0 + - + +
119A ALA* 3.8 20.9 - - + -
122A ASP* 3.1 35.9 - - + -
123A ILE* 3.4 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR 4.0 0.2 - - - +
44A VAL* 3.5 9.7 - - - +
45A PHE* 3.1 60.4 + + + +
47A VAL* 3.6 31.4 - - + -
57A ASP* 3.6 27.1 - - + -
58A PHE* 1.3 77.2 - - - +
60A ILE* 1.3 66.6 + - - +
61A ARG 4.2 0.4 - - - -
73A GLU* 5.2 9.0 - - + -
74A CYS 3.1 22.7 - - - +
75A MET* 3.6 29.2 - - + -
76A LEU* 4.4 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 3.7 25.6 - - + -
43A THR 3.5 4.9 - - - +
44A VAL* 4.6 6.5 - - + -
59A PHE* 1.3 77.4 - - - +
61A ARG* 1.3 65.0 + - - +
72A LEU* 3.5 8.4 - - + +
73A GLU* 3.2 7.6 - - - +
74A CYS* 2.9 40.5 + - + +
76A LEU* 3.7 30.5 - - + -
80A LEU* 5.5 1.1 - - + -
92A TRP* 3.9 40.4 - - + -
112A PHE* 4.2 9.0 - - + -
116A ILE* 4.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER 3.7 0.9 - - - +
42A VAL* 3.3 5.4 - - - +
43A THR* 2.7 45.6 + - - +
45A PHE* 3.5 35.0 - - + -
59A PHE 4.2 0.2 - - - -
60A ILE* 1.3 76.1 - - - +
62A GLY* 1.3 63.3 + - - +
63A GLU* 4.0 24.4 + - + -
70A VAL* 3.2 31.8 - - + +
72A LEU 3.3 6.5 - - - +
73A GLU* 2.9 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER* 4.4 4.9 - - - -
41A SER 3.5 9.2 - - - -
42A VAL* 4.2 9.0 - - - -
61A ARG* 1.3 76.1 - - - +
63A GLU* 1.3 63.1 + - - -
70A VAL* 3.4 3.9 - - - -
71A VAL* 2.8 37.1 + - - +
72A LEU* 3.1 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 6.0 0.5 + - - -
40A SER* 3.2 3.7 - - - -
41A SER* 3.1 40.6 + - - +
43A THR* 6.1 0.7 - - - +
61A ARG* 4.0 33.8 + - + +
62A GLY* 1.3 77.7 - - - +
64A ARG* 1.3 64.8 + - - +
65A LEU* 3.4 0.7 + - - +
68A LYS* 3.3 38.2 - - - +
69A MET 3.2 9.6 - - - +
70A VAL* 4.3 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER 5.5 0.2 - - - +
38A GLY* 5.5 1.3 - - - -
39A LEU 3.7 4.9 - - - +
40A SER* 3.6 14.5 + - - +
62A GLY 4.3 0.4 + - - -
63A GLU* 1.3 72.3 - - - +
65A LEU* 1.3 60.7 + - - +
66A ARG* 4.0 26.7 - - + +
67A ASP* 3.4 17.9 - - - +
68A LYS* 2.8 28.9 + - - -
69A MET* 3.1 13.4 + - + +
71A VAL* 4.4 9.5 - - + +
----------------------------------------------------------
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