Contacts of the strand formed by residues 223 - 242 (chain A) in PDB entry 4IYT
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 223 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP* 3.6 7.4 - - - +
221A GLY* 3.3 5.6 - - - +
222A ASP* 1.3 89.2 + - + +
224A SER* 1.3 67.7 + - - +
270A GLU* 3.7 30.7 + - - +
271A VAL 3.1 10.3 - - - +
272A ASN* 3.9 19.1 - - - +
273A TRP* 4.2 1.1 - - - -
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Residues in contact with SER 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 4.7 0.4 - - - -
86A ASP* 2.5 30.6 + - - -
89A VAL* 3.4 12.8 - - - +
216A HIS* 3.8 0.7 - - - -
223A THR* 1.3 71.9 + - - +
225A GLU* 1.3 64.6 + - - +
226A PHE* 3.9 21.1 - - - -
269A TYR 3.8 0.2 - - - +
270A GLU* 3.3 2.7 - - - -
271A VAL* 2.9 30.9 + - - -
273A TRP* 2.8 27.7 + - - +
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 2.8 34.4 + - - -
85A ASN* 4.0 27.3 + - - +
86A ASP* 5.1 1.0 - - - +
224A SER* 1.3 76.5 - - - +
226A PHE* 1.3 61.8 + - - +
268A LYS* 3.4 34.7 + - + +
269A TYR 3.2 8.7 - - - +
270A GLU* 4.1 17.2 - - + +
281A LYS* 4.1 14.9 - - - +
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Residues in contact with PHE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 5.7 0.2 - - + -
46A LEU* 4.3 6.1 - - + -
48A LEU* 4.8 9.6 - - + -
82A LEU* 3.8 27.4 - - + -
83A LYS 3.2 5.6 - - - -
84A THR* 3.7 24.2 - - + -
89A VAL* 4.1 10.5 - - + -
214A VAL* 3.7 40.4 - - + -
224A SER* 3.9 18.2 - - - -
225A GLU* 1.3 74.4 - - - +
227A GLU* 1.3 60.0 + - - +
228A ILE* 4.1 4.0 - - + -
267A VAL 3.7 1.0 - - - +
268A LYS* 3.4 3.5 - - - -
269A TYR* 2.6 51.2 + - + +
271A VAL* 3.9 38.1 - - + -
273A TRP* 4.2 6.3 - + - -
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLY 3.8 0.9 - - - +
82A LEU* 3.4 3.6 - - - -
83A LYS* 2.8 70.2 + - + +
226A PHE* 1.3 74.0 - - - +
228A ILE* 1.3 60.0 + - - +
229A THR* 4.2 2.4 + - + +
266A THR* 3.2 34.2 - - + +
267A VAL 3.3 7.4 - - - +
268A LYS* 4.3 21.9 - - + +
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 2.9 28.8 + - - +
31A ILE* 3.9 30.1 - - + -
33A PHE* 4.9 0.4 - - + -
48A LEU* 4.3 7.9 - - + -
50A MET* 4.1 17.9 - - + -
81A GLY 3.2 9.6 - - - +
82A LEU* 3.7 23.3 - - + -
226A PHE* 4.9 1.3 - - + -
227A GLU* 1.3 75.4 - - - +
229A THR* 1.3 62.2 - - - +
230A TYR* 3.5 29.2 - - + -
266A THR* 4.4 0.9 - - - -
267A VAL 2.8 26.5 + - - -
269A TYR* 3.7 24.9 - - + -
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Residues in contact with THR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASN* 4.3 1.6 - - + -
80A ILE* 3.4 2.9 - - - +
81A GLY* 2.8 43.5 + - - +
155A GLN* 3.7 24.2 - - - +
227A GLU* 5.6 2.7 - - + +
228A ILE* 1.3 71.6 - - - +
230A TYR* 1.4 67.1 + - - +
264A ASN* 3.3 30.1 + - - +
265A TYR 3.4 2.9 - - - -
266A THR* 2.9 25.8 + - - -
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Residues in contact with TYR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 3.5 27.0 - - + +
28A THR 3.4 19.1 - - - -
29A GLN* 3.7 18.6 - - + +
31A ILE* 3.4 6.1 - - + +
50A MET* 3.2 24.8 - - + +
51A GLN 2.6 30.4 + - - -
54A ILE* 3.7 16.4 - - + -
79A ASN 3.3 5.2 - - - -
80A ILE* 3.7 22.0 - - + -
208A PRO* 3.7 16.6 - - + -
228A ILE* 3.5 21.1 - - + -
229A THR* 1.4 83.9 + - - +
231A GLY* 1.3 57.9 + - - +
264A ASN* 4.1 2.2 - - - -
265A TYR* 2.8 36.0 + - - +
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Residues in contact with GLY 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 5.0 1.8 - - - -
54A ILE* 3.8 11.0 - - - +
78A TYR* 3.3 11.1 - - - +
79A ASN 2.8 29.9 + - - +
230A TYR* 1.3 76.2 - - - +
232A ARG* 1.3 66.8 + - - +
263A ARG 3.2 8.5 - - - -
264A ASN* 3.1 16.1 + - - -
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Residues in contact with ARG 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS 5.4 0.4 + - - -
25A TRP* 2.8 41.4 + - - +
26A GLY 4.0 3.0 + - - -
27A VAL* 4.3 1.9 - - - +
54A ILE* 3.4 14.4 - - + +
55A ASN 2.8 36.6 + - - -
56A SER 3.5 16.8 - - - -
57A LYS* 3.5 20.2 - - - +
75A PRO* 4.1 4.3 - - + -
77A GLN 3.3 8.5 - - - +
78A TYR* 3.8 20.0 - - + -
79A ASN* 3.6 3.1 + - - +
231A GLY* 1.3 79.5 - - - +
233A ASN* 1.3 64.9 + - - +
234A MET* 3.7 22.5 - - + -
263A ARG* 2.8 59.1 + - + +
264A ASN* 3.3 1.4 + - - -
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Residues in contact with ASN 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PRO* 3.5 2.3 - - - +
76A PHE* 2.9 27.7 + - + -
77A GLN* 2.8 43.9 + - + +
79A ASN* 3.0 19.1 + - - -
147A GLU* 5.0 2.2 + - - -
232A ARG* 1.3 69.7 - - - +
234A MET* 1.3 61.0 + - - +
235A ASP* 5.3 0.2 - - - -
258A ASN* 4.4 17.1 - - - +
260A PHE 3.5 4.9 - - - -
261A VAL* 4.0 17.2 - - + +
262A ASN* 2.8 29.4 + - - +
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Residues in contact with MET 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A SER 3.5 18.4 - - - +
57A LYS* 3.7 21.1 - - + +
73A ARG* 3.9 28.5 - - + +
74A TRP* 3.4 22.4 - - - +
75A PRO* 3.8 9.2 - - - -
232A ARG* 3.7 32.3 - - - -
233A ASN* 1.3 72.1 - - - +
235A ASP* 1.4 61.5 + - - +
258A ASN 3.8 0.7 - - - -
259A ALA* 3.0 23.6 + - - +
260A PHE* 2.7 35.0 + - + +
263A ARG* 4.2 16.2 - - + -
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Residues in contact with ASP 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ARG* 3.4 4.7 - - - +
74A TRP* 2.9 46.5 + - + +
76A PHE* 3.4 16.6 - - + +
233A ASN 4.1 1.0 + - - -
234A MET* 1.4 74.1 - - - +
236A VAL* 1.3 64.4 + - - +
237A THR 4.2 0.2 - - - -
255A ARG* 2.7 38.9 + - - -
256A ILE 3.5 10.5 - - - +
257A HIS* 2.9 22.3 + - - -
258A ASN* 2.9 21.3 + - - -
259A ALA* 4.3 0.2 - - - -
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A TYR* 3.5 24.2 - - - +
71A ALA* 4.0 9.9 - - + -
72A MET 3.4 4.7 - - - +
73A ARG* 3.9 19.3 - - + -
235A ASP* 1.3 77.5 - - - +
237A THR* 1.3 63.4 + - - +
238A HIS* 3.6 27.6 + - + +
255A ARG* 3.5 3.9 - - - -
256A ILE* 2.9 42.1 + - + +
259A ALA* 3.8 19.5 - - + -
260A PHE* 4.1 9.0 - - + -
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Residues in contact with THR 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ALA* 3.3 3.6 - - - +
72A MET* 2.8 39.8 + - - -
74A TRP* 3.0 27.0 + - - +
175A PRO 4.3 3.6 - - - +
177A LEU 3.8 14.1 + - - +
179A VAL* 3.6 31.0 - - + -
192A PHE* 3.6 16.4 - - + -
235A ASP 4.2 0.2 - - - -
236A VAL* 1.3 71.8 - - - +
238A HIS* 1.3 62.4 + - - +
254A SER 3.5 8.3 - - - +
255A ARG* 3.5 17.3 + - - -
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Residues in contact with HIS 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A TYR* 4.8 1.8 + - - -
63A TYR* 3.6 33.7 - + - -
69A ILE* 4.2 18.6 - - + -
70A LYS 3.4 2.0 - - - +
71A ALA* 3.6 20.4 - - + +
236A VAL* 3.6 24.8 + - + +
237A THR* 1.3 76.6 - - - +
239A ALA* 1.3 59.1 + - - +
240A THR* 4.1 3.4 - - + -
252A GLU 3.6 1.2 - - - +
253A GLY* 3.5 5.4 - - - -
254A SER* 2.8 51.5 + - - +
256A ILE* 3.9 24.1 - - + +
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Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ILE* 3.5 1.9 - - - -
70A LYS 2.7 33.9 + - - -
179A VAL* 4.1 13.5 - - + -
191A TYR* 3.6 32.1 - - + +
192A PHE* 3.6 27.5 - - + -
238A HIS* 1.3 71.7 - - - +
240A THR* 1.3 61.3 + - - +
241A ARG 4.1 0.2 - - - -
251A LEU* 4.8 2.7 - - + -
252A GLU 3.7 5.4 - - - -
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Residues in contact with THR 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A HIS* 3.5 7.4 - - + -
69A ILE* 3.7 37.9 - - + -
238A HIS* 4.9 6.3 - - + +
239A ALA* 1.3 71.7 - - - +
241A ARG* 1.4 63.1 + - - +
242A ARG* 3.5 34.9 + - - +
251A LEU* 3.4 4.7 - - - -
252A GLU* 3.0 37.2 + - - +
254A SER* 5.2 4.5 - - - +
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Residues in contact with ARG 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A HIS* 2.7 45.3 + - + +
183A PRO* 4.1 11.4 - - + -
186A GLN* 4.9 7.4 - - - +
191A TYR* 3.5 26.5 - - + +
239A ALA 4.0 0.2 + - - -
240A THR* 1.4 70.3 - - - +
242A ARG* 1.3 66.9 + - - +
243A THR* 5.8 2.0 - - + -
249A SER* 4.0 27.1 - - - -
250A TYR 3.5 6.5 - - - +
251A LEU* 3.8 10.1 - - + +
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Residues in contact with ARG 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A HIS* 5.8 1.8 - - + -
240A THR* 3.5 22.6 + - - +
241A ARG* 1.3 79.1 - - - +
243A THR* 1.3 64.8 + - - +
249A SER* 3.3 5.2 - - - -
250A TYR* 2.8 61.7 + - + +
252A GLU* 3.4 37.8 + - - +
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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) + - + + + + + -
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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