Contacts of the strand formed by residues 223 - 232 (chain B) in PDB entry 1NYE
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 ILE 223 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG 3.9 19.3 - - - +
60A PHE* 4.0 33.0 - - + +
62A GLY 6.4 0.2 - - - +
69A GLU* 5.9 1.1 - - + -
104A VAL 3.3 2.9 - - - +
105A SER* 3.4 3.5 - - - -
106A LEU* 2.8 60.2 + - + +
113A PHE* 4.5 2.0 - - + -
221B MET* 4.1 23.8 - - + +
222B THR* 1.3 75.8 + - - +
224B HIS* 1.3 64.8 + - - +
225B LYS* 3.6 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASP* 2.9 35.3 + - - +
104A VAL 3.4 2.8 + - - -
105A SER* 3.0 27.9 + - - -
222B THR* 3.4 31.7 + - + +
223B ILE* 1.3 74.7 - - - +
225B LYS* 1.3 76.4 + - - +
226B LYS* 5.2 7.1 - - - +
245B GLU* 3.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR 2.6 31.5 + - - -
59A ARG 3.6 13.7 + - - -
62A GLY* 5.0 15.6 - - - -
63A GLU 5.0 2.3 + - - -
65A GLY 5.3 0.4 + - - -
67A ASN* 2.9 41.5 + - - +
69A GLU* 3.6 16.5 + - + +
70A GLU* 3.9 4.7 - - + +
103A ASP* 4.2 0.2 + - - -
104A VAL* 2.8 36.2 + - - +
223B ILE* 3.6 18.6 - - + -
224B HIS* 1.3 94.7 - - - +
226B LYS* 1.3 63.3 + - - +
245B GLU* 2.9 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU* 3.9 12.4 - - - +
101A THR* 4.1 20.7 - - + +
102A ALA 3.3 6.5 - - - +
103A ASP* 4.1 30.0 + - - +
224B HIS* 5.2 6.1 - - - -
225B LYS* 1.3 81.3 - - - +
227B GLY* 1.3 60.9 + - - +
245B GLU* 2.9 54.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU 3.9 3.1 - - - -
73A GLY* 3.7 9.7 - - - -
74A ALA* 3.6 21.5 - - - -
77A ALA* 4.4 0.2 - - - -
101A THR* 3.5 5.9 - - - +
102A ALA 2.9 29.9 + - - +
226B LYS* 1.3 74.6 - - - +
228B GLN* 1.3 61.7 + - - +
243B SER 3.5 10.5 - - - -
244B THR* 4.5 0.4 - - - -
245B GLU 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 4.3 2.5 - - - +
77A ALA* 3.9 4.7 - - - +
99A ASP* 4.4 13.1 + - - +
100A THR 3.1 18.9 + - - +
101A THR* 3.1 20.7 + - + +
227B GLY* 1.3 72.8 - - - +
229B ALA* 1.3 80.4 + - - +
230B HIS* 5.0 1.9 - - - +
242B VAL* 3.4 4.2 - - - +
243B SER* 2.7 49.6 + - - +
244B THR 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA* 3.6 8.5 - - + +
78A ALA* 3.5 35.7 - - + +
81A SER* 4.1 5.9 + - - +
98A ILE 3.7 1.0 - - - +
99A ASP* 3.8 0.5 - - - -
100A THR 3.0 31.1 + - - +
228B GLN* 1.3 86.5 - - - +
230B HIS* 1.3 60.9 + - - +
241B THR 3.0 13.2 - - - +
242B VAL* 4.0 3.8 - - + -
243B SER* 4.6 0.9 - - - +
254B TYR* 4.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 5.1 1.3 - - - -
97A SER* 3.3 24.4 + - - -
98A ILE 3.2 7.9 + - - -
99A ASP* 2.6 32.9 + - - +
228B GLN* 5.0 2.0 - - - +
229B ALA* 1.3 75.2 - - - +
231B TRP* 1.3 69.9 + - - +
232B GLU* 3.0 36.3 + - + +
239B LYS 5.5 1.1 - - - -
240B GLY* 3.1 4.8 - - - -
241B THR* 2.7 49.0 + - + +
251B GLN* 4.6 9.2 - - - +
254B TYR* 4.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 4.0 14.1 - - - -
82A MET* 4.1 21.8 - - + -
85A SER* 3.2 20.2 + - - -
95A PRO* 4.6 0.4 - - + +
97A SER* 3.5 1.7 - - - -
98A ILE* 2.9 51.8 + - + +
230B HIS* 1.3 76.6 + - - +
232B GLU* 1.3 85.4 + - - +
233B GLY 2.9 26.7 + - - -
234B ASP 3.5 7.3 + - - -
235B ILE* 3.6 22.4 - - - -
238B GLY* 3.8 18.6 - - - -
239B LYS 3.6 8.5 - - - -
240B GLY* 3.7 12.1 - - - -
254B TYR* 3.5 33.9 - + - -
255B GLY* 3.9 26.2 - - - -
256B PHE 3.9 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO 4.3 0.2 - - - -
96A THR 3.8 18.8 - - - +
97A SER* 5.2 0.4 - - - +
230B HIS* 3.0 30.3 + - + +
231B TRP* 1.3 84.4 + - - +
233B GLY* 1.3 66.0 + - - +
238B GLY* 3.3 22.0 - - - -
239B LYS* 3.0 20.9 + - + +
----------------------------------------------------------
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