Contacts of the strand formed by residues 76 - 85 (chain B) in PDB entry 1F5J
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 SER 76 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TRP* 3.6 15.1 - - - -
70B TYR* 2.6 32.5 + - - -
72B PRO* 3.5 21.5 - - - -
74B GLY 3.1 2.8 + - - -
75B ASN* 1.3 82.8 + - - +
77B TYR* 1.3 73.0 + - - +
97B TRP* 3.1 3.3 - - - +
98B GLY 3.0 19.8 + - - +
179B VAL* 4.4 0.2 - - - +
180B GLU 2.6 22.3 + - - -
181B GLY* 4.3 0.4 - - - -
182B TYR 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B TYR* 3.1 10.6 + - - -
75B ASN* 3.9 19.8 + - - -
76B SER* 1.3 94.6 + - - +
78B LEU* 1.3 59.7 + - - +
79B CYS* 3.9 11.2 - - + -
92B TYR* 3.9 11.2 - + - -
94B VAL* 4.5 6.7 - - + -
96B SER 3.6 6.1 - - - +
97B TRP* 4.3 1.6 - - + -
100B TRP* 3.4 24.3 - + - -
102B PRO* 3.5 40.1 - - + +
103B PRO* 5.2 0.2 - - - +
141B TRP* 3.9 22.6 - + - -
178B CYS 3.7 0.4 - - - +
179B VAL* 3.4 4.9 - - - -
180B GLU* 2.9 67.6 + - + +
182B TYR* 6.1 2.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR* 4.3 11.9 - - + -
68B ALA* 4.6 8.7 - - + -
70B TYR* 3.5 26.2 + - + -
77B TYR* 1.3 72.3 - - - +
79B CYS* 1.3 63.9 + - - +
94B VAL* 3.8 0.5 - - - -
95B GLU* 2.9 27.4 + - + -
96B SER* 2.9 16.7 + - - +
148B ARG 3.9 7.6 - - - +
149B THR* 3.9 39.3 - - + +
177B LEU* 4.5 15.0 - - + -
178B CYS 3.5 8.1 - - - +
179B VAL* 4.0 17.9 - - + -
190B ILE* 4.7 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 4.4 9.4 - - + -
78B LEU* 1.3 79.3 - - - +
80B ILE* 1.3 69.2 + - - +
81B TYR* 4.0 10.8 - - - -
92B TYR* 3.6 28.3 - - + -
93B ILE 3.2 15.0 - - - +
94B VAL* 3.8 14.8 - - + -
95B GLU* 4.3 3.8 - - - +
177B LEU* 3.5 6.7 - - - +
178B CYS* 2.6 59.9 + - - +
180B GLU* 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.9 29.8 - - + -
66B TYR* 5.2 2.9 - - + -
79B CYS* 1.3 76.5 - - - +
81B TYR* 1.3 63.1 + - - +
91B PHE* 5.2 4.2 - - + -
92B TYR* 3.4 4.7 - - - -
93B ILE* 2.9 50.4 + - + +
95B GLU* 5.2 2.0 - - + -
153B VAL* 3.8 32.8 - - + -
155B VAL* 4.0 22.0 - - + -
175B ILE* 4.0 14.8 - - + -
176B THR 3.1 11.0 - - - +
177B LEU* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.6 23.9 - - + +
47B ARG* 3.4 45.2 + - - -
79B CYS* 4.0 3.6 - - - -
80B ILE* 1.3 77.1 - - - +
82B GLY* 1.3 57.9 + - - +
83B TRP* 2.8 30.4 + + - -
90B GLU* 2.6 40.8 + - + -
91B PHE* 3.4 15.0 - - - -
92B TYR* 3.7 26.0 - + - -
174B GLN* 4.8 0.2 - - - -
175B ILE 3.6 0.2 - - - -
176B THR* 2.7 47.0 + - - +
178B CYS* 3.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 1.3 82.4 - - - +
83B TRP* 1.3 72.7 + - - -
90B GLU* 3.5 3.3 - - - +
91B PHE* 2.9 43.4 + - - +
174B GLN* 3.2 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ARG* 4.2 3.8 - - - +
81B TYR* 2.8 28.1 + + - -
82B GLY* 1.3 78.6 - - - -
84B SER* 1.3 60.7 + - - +
88B LEU* 3.7 24.0 - - + -
89B VAL 3.1 20.2 - - - -
90B GLU* 3.4 29.4 - - + -
91B PHE* 3.3 8.7 - - - -
129B PRO 3.9 3.1 - - - -
130B SER* 3.5 33.7 - - - -
131B ILE* 3.4 41.3 - - + +
137B PHE* 3.4 38.1 - + - -
172B ILE* 3.7 3.6 - - - -
173B ASP* 2.8 22.9 + - + -
174B GLN* 3.3 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TRP* 1.3 75.0 - - - +
85B THR* 1.3 63.9 + - - +
87B PRO 2.8 14.6 + - - -
88B LEU* 3.2 11.3 - - - +
89B VAL* 2.9 38.9 + - - +
169B LEU* 3.5 15.7 - - - +
170B GLY 3.4 24.3 + - - -
171B THR 3.0 14.4 - - - -
172B ILE* 4.1 3.1 - - - -
173B ASP 4.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ASN* 5.6 0.5 + - - -
84B SER* 1.3 78.2 - - - +
86B ASN* 1.3 77.7 + - - +
87B PRO 3.0 4.8 - - - +
88B LEU* 4.0 5.2 - - + +
131B ILE* 3.7 24.9 - - + -
132B VAL* 4.3 17.0 - - + -
171B THR* 2.8 42.3 + - - +
173B ASP* 4.9 5.6 - - + +
----------------------------------------------------------
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