Contacts of the strand formed by residues 73 - 82 (chain B) in PDB entry 6FF8
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 THR 73 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B THR* 3.7 1.4 + - - -
22B ARG* 3.4 4.0 - - + +
24B HIS* 3.7 32.1 - - + +
68B ASN* 3.9 0.9 - - - -
69B TRP* 3.0 47.5 + - + +
70B ASP* 2.7 34.3 + - - +
71B SER 3.5 0.4 - - - -
72B ARG* 1.3 84.8 + - - +
74B LEU* 1.3 62.6 + - - +
75B VAL* 4.4 4.5 - - + -
193B LEU* 4.6 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B THR* 4.7 2.4 + - - +
22B ARG 2.8 11.7 + - - +
23B GLU* 3.2 17.1 - - + +
24B HIS* 2.9 26.9 + - - +
66B VAL* 4.3 15.3 - - + -
67B LEU 3.6 5.8 - - - +
68B ASN* 3.2 30.3 - - - +
73B THR* 1.3 74.0 - - - +
75B VAL* 1.3 63.6 + - - +
76B ARG* 3.6 48.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B HIS* 3.6 16.6 - - - +
26B PHE* 3.7 30.5 - - + -
66B VAL* 3.6 1.6 - - - -
67B LEU* 2.7 52.3 + - + +
69B TRP* 4.0 21.5 - - + -
73B THR* 4.0 3.8 - - + -
74B LEU* 1.3 78.5 - - - +
76B ARG* 1.3 63.6 + - - +
77B LEU* 3.7 21.3 + - + -
189B VAL* 4.1 19.3 - - + -
193B LEU* 4.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASN* 4.7 6.3 + - - -
91A MET* 2.8 50.9 - - - +
94A VAL* 3.7 31.8 - - - +
23B GLU* 2.8 35.8 + - - +
24B HIS 2.7 14.8 + - - +
25B LEU* 3.2 19.3 - - + +
26B PHE 2.8 30.8 + - - -
64B LEU* 4.5 7.9 - - + -
65B LYS 3.3 6.5 - - - +
66B VAL* 4.4 11.7 - - + +
74B LEU* 3.6 25.2 - - + +
75B VAL* 1.3 79.4 - - - +
77B LEU* 1.3 57.2 + - - +
78B GLN 4.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.3 25.1 - - + +
28B VAL* 3.9 16.6 - - + -
45B TYR* 4.4 17.3 - - + +
64B LEU* 3.2 8.2 - - - +
65B LYS* 2.8 40.2 + - + +
67B LEU* 4.3 14.8 - - + -
75B VAL* 3.7 22.7 - - + -
76B ARG* 1.3 71.9 - - - +
78B GLN* 1.3 60.5 + - - +
79B LEU* 3.5 23.5 + - + +
103B PHE* 6.2 2.2 - - + -
185B ALA* 5.3 3.4 - - + -
189B VAL* 4.2 21.8 - - + -
192B ILE* 5.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 4.8 3.6 - - - +
80A TRP* 3.2 35.1 - - + -
94A VAL* 5.4 3.2 + - - +
25B LEU* 3.7 34.8 - - + +
26B PHE 2.8 10.0 + - - +
27B LYS* 3.5 15.0 + - - +
28B VAL 2.9 28.9 + - - +
63B ALA 3.7 5.8 - - - +
64B LEU* 3.5 17.6 - - + +
76B ARG 4.1 0.2 - - - -
77B LEU* 1.3 70.7 - - - +
79B LEU* 1.3 59.1 + - - +
80B TRP* 3.6 18.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.5 31.4 - - + +
30B VAL* 4.3 12.6 - - + -
42B ILE* 4.4 21.4 - - + +
45B TYR* 4.5 12.6 - - + -
46B VAL* 3.9 28.0 - - + -
61B ASP 3.8 0.2 - - - +
62B PHE* 3.1 9.9 - - - +
63B ALA* 2.8 39.3 + - + +
65B LYS* 4.3 15.3 - - + +
77B LEU* 3.5 14.3 + - + -
78B GLN* 1.3 69.9 - - - +
80B TRP* 1.3 62.6 + - - +
81B ASP* 3.8 1.1 + - - +
103B PHE* 4.8 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.0 25.8 - - + -
78A GLN* 3.7 19.0 - - - +
27B LYS* 3.5 37.1 - - + +
28B VAL 2.9 8.2 + - - +
29B LEU* 3.6 17.5 - - + -
30B VAL* 2.9 31.0 + - - -
60B VAL* 4.0 11.2 - - + -
61B ASP 3.7 4.3 - - - -
62B PHE* 3.6 28.0 - + - -
78B GLN* 3.7 26.9 + - + +
79B LEU* 1.3 73.4 - - - +
81B ASP* 1.3 55.2 + - - +
82B ILE* 3.6 8.9 + - + +
94B VAL 5.3 1.1 - - - -
95B TYR* 3.4 39.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL 3.9 3.6 - - - -
38B LYS* 3.3 24.6 - - - +
39B THR* 2.4 34.3 + - - +
42B ILE* 3.4 27.8 - - + +
57B THR* 3.8 4.3 + - - +
60B VAL* 3.3 5.3 - - - -
61B ASP* 2.9 54.9 + - + +
62B PHE* 5.3 0.7 - - - -
79B LEU 3.8 1.6 + - - +
80B TRP* 1.3 67.6 - - - +
82B ILE* 1.3 63.1 + - - +
83B ALA 3.6 0.7 + - - -
901B MG 4.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.2 17.5 - - + -
30B VAL 3.2 9.2 + - - +
31B ILE* 3.7 24.7 - - + -
32B GLY 4.6 0.7 + - - +
38B LYS* 2.9 26.4 - - - +
59B GLY 3.9 3.1 - - - +
60B VAL* 3.9 17.7 - - + -
80B TRP* 3.9 11.2 - - + +
81B ASP* 1.3 72.1 - - - +
83B ALA* 1.3 64.0 + - - +
86B GLU* 3.6 29.6 - - + -
92B THR* 4.9 4.0 - - + -
95B TYR* 3.7 32.3 - - + -
96B TYR* 4.5 4.0 - - + -
120B TRP* 4.4 13.6 - - + -
----------------------------------------------------------
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