Contacts of the strand formed by residues 80 - 91 (chain A) in PDB entry 4FYT
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 80 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO 4.4 4.0 + - - +
78A ASN 4.5 2.6 - - - -
79A THR* 1.3 96.8 + - - +
81A LYS* 1.3 63.0 + - - +
82A PRO* 4.4 1.2 - - - +
111A PHE* 4.0 16.6 - - + -
112A THR 3.5 2.9 - - - +
113A CYS* 3.9 17.0 - - - -
114A LYS* 4.6 1.3 - - - -
117A THR* 3.9 9.9 - - + -
119A VAL 4.0 5.2 - - - +
120A ILE* 3.8 45.8 - - + -
121A ILE 4.5 3.1 - - - +
170A LEU* 3.9 19.7 - - + -
224A PHE* 4.1 22.2 - - + -
229A MET* 3.9 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 1.3 76.7 - - - +
82A PRO* 1.3 77.9 + - + +
83A ASP* 4.0 1.4 - - - +
111A PHE* 4.0 2.0 - - - -
112A THR* 2.8 36.8 + - - -
114A LYS* 4.0 31.2 - - + +
228A ALA 3.4 23.6 + - - -
229A MET* 4.4 12.9 - - - +
230A LYS 4.5 9.1 + - - +
274A LYS* 5.5 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 1.3 96.1 + - + +
83A ASP* 1.3 62.0 + - - +
85A TYR* 3.7 26.5 - - + +
109A VAL* 4.1 6.1 - - + -
111A PHE* 3.7 10.3 - - + -
224A PHE* 3.7 34.1 - - + -
229A MET* 3.7 40.6 - - + +
230A LYS 3.7 13.0 - - - +
231A ALA* 4.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS 4.3 1.5 - - - +
82A PRO* 1.3 77.6 - - - +
84A SER* 1.3 60.8 + - - +
110A ARG* 2.8 17.9 + - + +
111A PHE* 3.4 4.9 + - - -
112A THR* 2.8 37.8 + - - -
175A GLN* 2.9 23.6 + - - +
231A ALA* 3.4 8.3 - - - +
232A GLU* 3.2 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PRO 4.0 0.2 - - - -
83A ASP* 1.3 82.6 - - - +
85A TYR* 1.3 65.8 + - - +
109A VAL* 3.5 2.8 - - - +
110A ARG* 2.8 37.9 + - - +
231A ALA* 4.1 2.2 - - - +
232A GLU* 3.2 27.6 - - - +
1C NAG 3.1 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PRO* 3.7 11.6 - - + +
84A SER* 1.3 78.7 - - - +
86A ARG* 1.3 59.9 + - - +
87A VAL* 4.4 7.2 - - + -
107A SER* 4.3 6.7 - - - -
108A THR 3.3 7.6 - - - +
109A VAL* 3.5 31.6 - - + -
221A PHE* 3.9 11.9 - + - -
222A PRO 3.9 3.1 - - - -
223A CYS* 3.6 26.4 - - + +
224A PHE* 2.9 39.6 + + - +
229A MET 5.4 0.7 - - - -
231A ALA* 3.6 21.3 - - + -
232A GLU 2.9 5.3 + - - -
233A PHE* 3.1 40.2 - + + -
234A ASN* 2.8 30.7 + - - +
277A THR* 4.6 1.9 - - + +
1C NAG 3.7 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 1.3 74.4 - - - +
87A VAL* 1.3 62.1 + - - +
107A SER* 2.9 20.9 + - - -
108A THR* 2.9 55.8 + - - +
140A ARG* 4.1 11.1 - - - +
177A GLU* 4.6 6.7 + - - -
179A ASP* 5.7 0.2 - - - -
234A ASN* 3.2 17.5 - - + +
1C NAG 2.8 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 4.4 7.9 - - + -
86A ARG* 1.3 80.3 - - - +
88A THR* 1.3 63.5 + - - +
89A LEU* 3.8 27.1 - - + -
106A SER 3.5 10.5 - - - +
107A SER* 3.6 11.4 - - - +
221A PHE* 3.6 48.5 - - + -
233A PHE* 5.1 0.7 - - + -
234A ASN 3.0 7.8 + - - +
235A ILE* 3.5 21.8 - - + +
236A THR* 2.9 26.5 + - - +
282A PHE* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 1.3 73.4 - - - +
89A LEU* 1.3 65.3 + - - +
90A ARG* 5.8 0.4 - - + -
104A LYS 5.7 0.2 - - - +
105A GLY* 3.0 6.5 - - - -
106A SER* 2.9 50.0 + - - +
236A THR* 3.3 28.1 + - + +
238A ILE* 3.6 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 3.8 15.3 - - + -
88A THR* 1.3 83.6 - - - +
90A ARG* 1.3 61.2 + - - +
91A PRO* 4.0 2.7 - - - +
103A PHE* 4.0 11.7 - - + -
104A LYS 3.6 1.3 - - - -
105A GLY* 3.9 3.8 - - - -
182A PHE* 3.7 15.0 - - + -
193A PHE* 4.1 21.5 - - + -
220A SER* 3.6 27.6 - - - +
235A ILE* 6.3 0.4 - - + -
236A THR 3.0 6.7 + - - -
237A LEU* 3.4 19.0 - - + +
238A ILE* 3.0 24.1 + - - +
282A PHE* 3.4 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A THR* 5.8 0.2 - - + -
89A LEU* 1.3 76.2 - - - +
91A PRO* 1.3 63.9 - - - +
92A TYR* 3.3 35.4 + - + -
103A PHE* 3.2 3.4 - - - +
104A LYS* 2.8 40.1 + - + +
238A ILE* 3.5 34.6 - - + +
258A LEU* 3.7 25.5 - - - +
260A GLU* 3.7 15.8 + - - -
261A ASP* 4.9 4.0 + - - +
264A TRP* 3.3 55.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU 4.0 3.4 - - - +
90A ARG* 1.3 85.5 - - - +
92A TYR* 1.3 60.7 + - - +
93A LEU* 3.9 11.7 + - + +
103A PHE* 3.9 8.9 - - + -
186A LEU* 4.1 10.8 - - + -
193A PHE* 3.9 20.2 - - + -
208A ALA* 3.7 31.6 - - + -
237A LEU* 5.7 1.3 - - + -
238A ILE 3.4 13.7 - - - +
239A HIS* 5.4 1.6 - - + -
240A PRO* 4.8 1.3 - - + +
264A TRP* 3.4 21.0 - - - -
284A VAL* 4.1 20.6 - - + -
----------------------------------------------------------
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