Contacts of the strand formed by residues 89 - 100 (chain B) in PDB entry 4FPR
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 LEU 89 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU* 3.8 20.0 - - - +
31B ILE 3.7 3.4 - - - -
32B ARG* 3.4 28.9 - - + -
76B CYS* 3.5 1.0 - - - -
77B ALA* 2.9 37.8 + - + +
87B VAL* 3.6 21.7 + - + +
88B VAL* 1.3 74.2 - - - +
90B CYS* 1.3 61.7 + - - +
91B THR 4.3 0.2 - - - -
123B THR* 4.1 15.3 - - + +
135C MET* 4.0 33.9 - - + +
136C LYS* 3.9 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU* 3.4 7.2 - - - +
31B ILE* 2.7 48.1 + - + +
33B TYR* 3.8 25.8 - - + +
39B PRO* 4.9 0.7 - - - -
44B ALA* 4.2 3.1 - - + -
74B VAL* 4.0 10.1 - - + -
75B GLN 3.3 4.7 - - - +
76B CYS* 2.0 47.6 - - - -
88B VAL* 3.8 7.2 - - - -
89B LEU* 1.3 76.1 - - - +
91B THR* 1.3 62.0 + - - +
92B CYS* 3.8 1.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 4.2 14.4 - - - +
29B GLY 3.6 9.2 - - - +
30B GLU* 4.8 4.0 + - - +
73B LYS 3.9 0.2 - - - +
74B VAL* 3.2 8.3 - - - +
75B GLN* 2.8 35.1 + - - +
90B CYS* 1.3 72.8 - - - +
92B CYS* 1.3 64.1 + - - +
93B LYS* 3.8 4.6 + - + +
122B GLU* 3.8 27.8 + - - +
136C LYS* 2.7 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE 3.7 2.1 - - - +
28B SER* 3.3 2.9 - - - -
29B GLY 2.8 37.1 + - - +
31B ILE* 4.3 13.7 - - + -
48B CYS* 2.1 63.0 - - + -
51B VAL* 3.9 9.9 - - - -
73B LYS 3.8 0.4 - - - -
74B VAL* 4.6 1.8 - - + -
90B CYS 3.8 1.2 + - - +
91B THR* 1.3 72.1 - - - +
93B LYS* 1.3 57.2 + - - +
94B ILE* 3.1 25.1 - - - +
119B PHE* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER* 3.7 30.7 - - - -
27B ILE 3.6 4.3 - - - +
28B SER* 3.7 19.7 - - - +
71B THR 3.8 0.9 - - - +
72B ALA* 3.5 1.7 - - - -
73B LYS* 2.9 60.6 + - + +
91B THR* 3.8 6.1 + - + +
92B CYS* 1.3 71.5 - - - +
94B ILE* 1.3 64.3 + - - +
95B THR* 4.4 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER* 3.2 3.9 - - - -
27B ILE* 2.9 38.1 + - + +
48B CYS* 3.9 0.2 - - - -
51B VAL* 3.4 20.9 - - + -
52B THR* 3.7 24.0 - - - +
55B LEU* 4.0 21.1 - - + -
70B MET* 4.0 29.2 - - + -
71B THR 3.4 5.6 - - - +
72B ALA* 4.4 2.7 - - + -
92B CYS* 3.1 41.5 - - - +
93B LYS* 1.3 76.1 - - - +
95B THR* 1.3 63.7 + - - +
119B PHE* 4.2 4.3 - - + -
131B TRP* 3.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 3.7 22.2 - - + -
25B ALA 3.4 11.0 - - - +
26B SER* 3.1 13.9 + - - +
70B MET* 3.1 5.2 - - - -
71B THR* 2.8 45.0 + - - -
73B LYS* 5.6 6.9 + - - +
93B LYS* 4.4 10.4 + - - +
94B ILE* 1.3 76.6 - - - +
96B ALA* 1.3 59.9 + - - +
97B HIS* 3.4 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ARG 4.1 1.2 - - - +
24B GLU* 3.4 4.7 - - - +
25B ALA 2.8 33.1 + - - +
66B TRP 3.5 23.6 - - - +
69B ASP 3.6 4.5 - - - -
70B MET* 3.8 8.3 - - + -
95B THR* 1.3 72.1 - - - +
97B HIS* 1.3 60.3 + - - +
98B ARG 3.6 0.7 - - - -
99B TYR* 4.2 12.8 - - + +
131B TRP* 3.6 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 3.5 45.5 - - + +
23B ARG 3.4 5.4 - - - +
24B GLU* 4.3 12.0 + - - +
69B ASP* 2.8 41.9 + - + +
71B THR* 2.6 31.5 + - + +
95B THR* 3.4 29.0 + - + +
96B ALA* 1.3 73.7 - - - +
98B ARG* 1.3 66.6 + - + +
140B ARG* 2.7 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A CYS* 5.6 1.8 - - - -
22B CYS* 3.5 14.4 - - - -
23B ARG 4.0 0.7 - - - -
66B TRP 4.2 4.8 + - - -
67B GLY* 3.2 27.5 + - - -
68B ILE 5.6 0.7 - - - +
69B ASP* 4.4 17.9 + - + +
96B ALA 3.6 0.2 - - - -
97B HIS* 1.3 87.7 - - + +
99B TYR* 1.3 57.2 + - - +
100B ARG* 4.0 3.6 + - - -
140B ARG* 4.3 9.6 - - + +
141B GLY* 3.2 40.8 + - - +
142B CYS 4.0 10.8 - - - +
143B ASP 3.4 32.2 + - - -
144B HIS* 3.1 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B CYS* 3.0 5.9 - - - +
23B ARG* 2.8 42.5 + - + +
25B ALA* 3.5 23.8 - - + -
65B ALA 3.9 3.1 - - - -
66B TRP* 3.2 43.4 + + + -
96B ALA* 4.2 15.3 - - + +
98B ARG* 1.3 71.8 - - - +
100B ARG* 1.3 81.1 + - - +
101B GLU* 3.3 5.8 + - + -
103B VAL 6.0 0.7 - - - -
105B LYS* 4.1 19.9 - - - +
106B ILE 5.3 0.2 + - - -
131B TRP* 3.2 38.4 - + + +
133B VAL* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL 4.2 0.4 - - - -
22B CYS* 3.2 8.2 - - - -
63B GLN* 2.9 23.4 + - - +
64B ARG* 3.0 36.0 + - - +
65B ALA* 3.0 27.2 + - - +
67B GLY* 4.5 5.7 - - - -
98B ARG 4.7 1.0 + - - +
99B TYR* 1.3 80.7 - - - +
101B GLU* 1.3 64.5 + - - +
102B PHE* 3.2 33.3 - - + -
103B VAL* 3.9 19.9 + - + +
142B CYS* 3.5 45.1 + - - +
143B ASP* 4.9 4.2 + - - -
----------------------------------------------------------
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