Contacts of the strand formed by residues 59 - 72 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H GLU* 1.3 71.7 - - - +
60H VAL* 1.3 60.7 - - - +
61H TRP* 5.8 2.4 - - + -
117H GLU* 4.0 22.4 - - + +
118H GLY 3.6 6.5 - - - +
119H VAL* 4.2 15.7 - - + -
140H GLN* 3.9 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H VAL 5.5 0.2 - - - -
46H VAL* 4.0 18.6 - - + -
51H LEU* 3.8 23.3 - - + -
55H LYS* 3.7 31.0 - - - +
58H GLU* 4.1 14.8 - - + +
59H VAL* 1.3 78.4 - - - +
61H TRP* 1.3 61.6 + - - +
62H VAL* 4.4 3.5 - - + +
116H VAL 3.8 0.9 - - - +
117H GLU* 3.6 3.1 - - - +
118H GLY 3.0 34.8 + - - +
120H VAL* 3.9 15.7 - - + -
137H LEU* 4.1 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H ARG* 3.5 57.6 - - + +
44H VAL 3.6 18.3 + - - +
45H LEU* 3.7 14.6 - - + -
46H VAL* 2.9 28.3 + - - +
59H VAL* 5.8 2.2 - - + -
60H VAL* 1.3 74.1 - - - +
62H VAL* 1.3 62.9 + - - +
115H ASP* 4.0 21.8 - - + -
116H VAL 3.2 11.9 - - - -
117H GLU* 3.5 61.7 + - + -
141H LYS* 4.2 12.8 - - + -
143H TYR* 4.1 20.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H LEU* 4.8 3.6 - - - +
46H VAL* 3.8 26.5 - - + +
48H VAL* 4.1 18.8 - - + -
51H LEU* 3.9 21.5 - - + -
60H VAL* 4.4 4.5 - - + -
61H TRP* 1.3 80.1 - - - +
63H ARG* 1.3 61.9 - - - +
64H ALA* 4.1 21.3 - - + -
80H LEU* 4.8 9.9 - - + -
82H GLN* 5.4 0.4 - - - +
87H VAL* 5.8 0.4 - - + -
114H VAL 3.5 2.8 - - - +
115H ASP* 3.5 1.1 - - - -
116H VAL* 2.7 47.1 + - + +
137H LEU* 4.4 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294G ALA* 6.1 0.2 - - - +
295G PHE 2.4 31.9 + - - -
296G ASN* 2.6 32.1 + - - +
297G TYR* 4.2 8.9 - - - -
464G PRO* 5.6 2.4 - - - +
465G PRO* 3.2 19.3 - - - +
35H ILE* 3.3 21.8 - - - +
45H LEU* 3.9 25.8 - - + +
46H VAL 4.9 1.6 + - - +
62H VAL* 1.3 72.6 - - - +
64H ALA* 1.3 62.1 + - - +
82H GLN* 4.2 19.8 + - - +
113H ILE* 3.7 17.1 - - + +
114H VAL 3.3 4.0 - - - +
115H ASP* 2.8 30.0 + - - +
145H ILE* 4.0 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H VAL* 4.4 5.8 - - + -
62H VAL* 3.9 12.9 + - + -
63H ARG* 1.3 73.7 - - - +
65H ARG* 1.3 59.9 + - - +
80H LEU* 3.8 30.5 - - + -
81H ARG 3.3 16.4 - - - +
82H GLN* 4.6 2.2 - - + -
113H ILE* 3.4 5.9 - - - +
114H VAL* 2.8 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258G ILE 4.7 0.6 + - - -
259G CYS 3.2 17.4 + - - -
261G ASP* 2.7 33.9 + - - +
462G GLY* 2.4 30.8 + - - -
464G PRO* 4.3 5.7 - - - +
64H ALA* 1.3 73.3 - - - +
66H VAL* 1.3 61.6 + - - +
67H HIS 3.5 0.9 + - - -
80H LEU* 3.3 8.2 - - - -
81H ARG* 2.9 66.4 + - - +
82H GLN* 6.1 0.7 - - - +
111H GLU* 3.1 29.7 + - - +
112H SER 3.4 5.6 - - - -
113H ILE* 3.9 18.9 - - + +
188H ARG* 3.0 26.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ARG* 1.3 70.7 - - - +
67H HIS* 1.3 62.2 + - - +
68H THR* 4.3 8.1 - - - +
69H SER* 3.8 29.6 - - - +
78H LEU* 4.0 21.5 - - + -
79H VAL 3.9 2.7 - - - -
80H LEU* 4.6 3.6 - - + -
108H ILE* 3.7 31.4 - - + +
109H ASN 4.5 4.7 - - - +
110H LYS* 3.9 3.8 - - - -
111H GLU* 2.9 25.5 + - - -
112H SER 3.1 17.3 + - - +
114H VAL* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ARG 3.5 2.4 + - - -
66H VAL* 1.3 74.3 - - - +
68H THR* 1.3 68.3 + - + +
79H VAL* 2.8 40.2 + - + +
81H ARG* 3.3 45.7 + - + -
86H ASN* 4.6 10.8 + - - -
110H LYS* 4.6 14.2 + - - +
111H GLU* 4.3 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H VAL* 3.6 4.7 - - - +
67H HIS* 1.3 87.6 - - + +
69H SER* 1.3 62.2 + - - +
70H ARG* 4.1 4.5 + - - +
77H PHE 4.3 0.3 - - - +
78H LEU* 3.5 1.2 - - - -
79H VAL* 2.8 51.2 + - + +
110H LYS* 4.5 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 69 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H VAL* 3.8 19.3 - - - +
68H THR* 1.3 75.3 + - - +
70H ARG* 1.3 60.9 + - - +
71H ALA 4.0 0.9 + - - -
76H CYS* 4.8 1.8 - - - -
77H PHE 3.4 9.9 - - - -
78H LEU* 4.2 11.4 - - - -
105H ALA 4.4 7.6 - - - -
106H ALA* 3.8 24.1 + - - +
108H ILE 4.0 9.0 + - - -
110H LYS* 5.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ASP* 5.8 4.0 + - - -
68H THR* 4.1 5.1 + - - +
69H SER* 1.3 72.5 - - - +
71H ALA* 1.3 62.3 + - - +
76H CYS* 3.8 0.6 - - - -
77H PHE* 2.8 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H SER 4.0 1.2 + - - +
70H ARG* 1.3 82.7 + - - +
72H LYS* 1.3 60.7 + - - +
73H GLY 4.3 1.1 - - - +
75H GLN 3.6 13.0 - - - +
76H CYS* 3.9 9.0 - - + +
77H PHE* 6.2 0.7 - - - -
102H VAL* 5.4 2.2 - - + +
106H ALA* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H ALA* 1.3 72.4 - - - +
73H GLY* 1.3 66.6 + - - +
74H LYS 3.1 4.5 + - - -
75H GLN* 3.1 19.9 + - + +
----------------------------------------------------------
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