Contacts of the strand formed by residues 287 - 299 (chain A) in PDB entry 1PH3
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 VAL 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A PHE* 3.7 10.8 - - - -
254A TYR* 3.2 11.7 - - + +
255A THR* 4.9 1.8 - - - -
256A LEU* 5.7 1.1 - - + +
277A THR 3.9 0.2 - - - +
278A TYR* 4.9 1.1 - - - -
279A ASP* 3.0 43.4 + - + +
282A SER* 3.5 25.1 - - - +
285A LYS* 3.3 30.8 + - + +
286A LYS* 1.3 80.3 - - - +
288A LEU* 1.3 74.8 + - - +
289A ILE* 4.8 2.9 - - + -
141B ASP* 5.6 0.9 - - - +
142B ASP* 4.6 19.1 - - + +
143B GLU* 5.1 0.7 - - + -
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Residues in contact with LEU 288 (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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214A LEU* 4.1 20.0 - - + -
224A PHE* 3.8 31.6 - - + -
226A VAL* 4.2 11.9 - - + -
245A LEU* 4.0 26.5 - - + -
253A PHE* 3.5 31.9 - - + -
254A TYR 2.7 10.5 + - - +
255A THR* 2.8 29.8 + - - +
256A LEU 4.4 2.3 + - - -
273A ILE* 4.7 4.9 - - + -
276A ALA* 4.5 12.3 - - + -
277A THR 3.4 7.4 - - - +
278A TYR* 4.7 0.9 - - - -
287A VAL* 1.3 83.2 - - - +
289A ILE* 1.3 59.9 + - - +
290A LEU* 4.1 0.8 + - + -
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Residues in contact with ILE 289 (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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276A ALA* 3.3 6.4 - - - -
277A THR* 2.8 51.2 + - - +
278A TYR 4.9 1.1 - - - +
279A ASP* 3.7 38.6 - - + +
287A VAL* 4.8 3.1 - - + -
288A LEU* 1.3 76.3 - - - +
290A LEU* 1.3 73.3 + - - +
291A SER* 5.3 2.3 + - - +
57B PHE* 6.0 0.4 - - + -
133B ARG* 3.8 27.4 - - - +
136B VAL* 4.7 22.9 - - + -
141B ASP* 6.0 0.4 - - - +
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Residues in contact with LEU 290 (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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255A THR* 3.5 22.9 + - + +
256A LEU 3.7 21.3 - - - +
261A LYS* 6.0 0.4 - - - +
262A PHE* 4.3 13.7 - - + -
273A ILE* 3.8 16.6 - - + -
275A SER 3.8 4.5 - - - +
276A ALA* 3.8 21.1 - - + -
288A LEU* 4.1 1.8 + - + -
289A ILE* 1.3 93.7 - - - +
291A SER* 1.3 65.4 + - - +
294A SER* 3.6 12.3 - - - +
296A ILE* 4.1 27.8 - - + -
4D G 5.1 0.7 + - - -
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Residues in contact with SER 291 (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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261A LYS* 3.3 7.6 + - - -
275A SER* 4.9 1.9 + - - -
277A THR* 6.1 1.2 - - - +
289A ILE* 5.3 2.6 + - - +
290A LEU* 1.3 75.8 - - - +
292A HIS* 1.3 66.8 + - - +
293A TYR* 3.1 29.7 + - - -
294A SER* 2.7 28.4 + - - -
4D G 3.3 33.3 + - - +
12D G 4.6 0.7 - - - -
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Residues in contact with HIS 292 (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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63A PHE* 3.7 4.7 - - - -
64A PRO 4.5 0.9 - - - +
65A TYR* 3.8 20.2 - - + +
66A LYS 3.8 7.2 - - - -
261A LYS* 3.0 15.3 + - - -
291A SER* 1.3 73.7 - - - +
293A TYR* 1.3 72.3 + + - +
294A SER 3.4 0.2 - - - -
4D G 2.8 56.2 + - - +
5D T 3.4 40.2 + + + +
12D G 3.0 62.3 + - - +
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Residues in contact with TYR 293 (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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62A THR* 3.6 8.1 - - - -
63A PHE* 2.9 30.4 + - - -
65A TYR* 3.6 30.7 - + + -
223A ASP* 5.8 0.9 - - - +
274A ARG* 4.8 1.2 - - - +
275A SER* 3.4 22.9 + - - -
291A SER* 3.7 18.0 + - - -
292A HIS* 1.3 99.1 - + - +
294A SER* 1.3 64.5 + - - +
3D G 3.4 70.5 + + + -
4D G 3.2 36.3 + + - -
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Residues in contact with SER 294 (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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63A PHE* 3.2 7.4 - - - +
261A LYS* 3.0 22.3 + - - -
262A PHE* 3.7 2.0 - - - -
273A ILE* 5.5 0.4 - - - -
274A ARG 3.2 8.5 - - - -
275A SER* 2.7 31.1 + - - -
290A LEU* 3.9 16.2 - - - -
291A SER* 2.7 38.0 + - - -
293A TYR* 1.3 83.0 - - - +
295A ASN* 1.3 60.7 + - - +
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Residues in contact with ASN 295 (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 ALA 3.1 28.5 + - - +
62A THR 3.7 8.4 + - - -
63A PHE* 3.6 22.1 - - - +
113A ILE* 2.9 31.8 + - - +
114A HIS* 4.9 2.4 + - - -
262A PHE* 3.5 15.9 - - - -
272A ARG 3.6 0.5 - - - +
273A ILE* 3.3 5.1 - - - +
274A ARG* 2.8 43.0 + - + +
293A TYR 3.8 0.2 + - - -
294A SER* 1.3 76.0 - - - +
296A ILE* 1.3 73.7 + - - +
297A ILE* 3.4 11.1 - - + +
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Residues in contact with ILE 296 (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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114A HIS* 3.7 1.7 - - - +
243A LEU* 3.8 25.4 - - + -
257A SER* 4.1 3.6 - - - +
262A PHE* 3.5 39.9 - - + -
264A HIS* 2.9 28.5 + - + +
265A VAL* 4.5 12.6 - - + -
271A VAL* 3.7 34.8 - - + -
272A ARG 3.5 2.9 - - - -
273A ILE* 4.2 15.3 - - + -
290A LEU* 4.1 18.2 - - + -
295A ASN* 1.3 86.0 + - - +
297A ILE* 1.3 65.7 + - - +
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Residues in contact with ILE 297 (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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59A ILE 5.5 0.2 - - - +
60A ASP* 4.3 11.0 - - - +
61A ALA 3.7 24.0 - - - +
113A ILE* 3.7 14.8 - - + +
114A HIS 3.1 2.0 - - - -
115A ARG* 3.3 8.1 - - - +
116A ALA* 3.0 40.6 - - + +
271A VAL* 3.2 3.5 - - - -
272A ARG* 2.6 57.3 + - + +
274A ARG* 5.1 2.2 - - + -
295A ASN* 3.4 31.2 - - + +
296A ILE* 1.3 80.5 - - - +
298A THR* 1.3 64.0 + - - +
299A PHE* 4.1 0.7 - - + -
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Residues in contact with THR 298 (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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114A HIS 2.9 13.5 + - - -
115A ARG* 3.5 15.0 - - - +
116A ALA* 2.7 32.2 + - - +
156A VAL* 4.3 4.3 - - - +
264A HIS* 4.1 28.2 - - + +
265A VAL* 6.1 0.4 - - - -
266A ARG 6.2 0.2 - - - +
269A GLU* 5.1 12.8 - - + +
270A VAL 3.9 8.5 - - - +
271A VAL* 3.6 23.3 - - + -
297A ILE* 1.3 74.2 - - - +
299A PHE* 1.3 63.6 + - - +
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Residues in contact with PHE 299 (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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115A ARG* 3.7 9.8 - - - -
116A ALA* 3.8 11.4 - - + -
200A PHE* 4.5 14.6 - + - -
204A SER 4.9 2.5 - - - -
206A ILE* 3.6 27.6 - - + -
227A VAL* 4.8 4.3 - - + -
270A VAL* 3.6 22.4 + - + -
271A VAL 3.9 5.4 - - - -
272A ARG* 3.8 40.2 - - + -
297A ILE 4.1 2.0 - - - -
298A THR* 1.3 81.7 - - - +
300A ILE* 1.3 65.7 + - + +
301A GLN* 3.7 0.7 + - - -
303A SER* 3.5 31.9 - - - +
305A LEU* 4.2 20.0 - - + -
306A ALA* 3.8 13.5 - - + +
310A ARG* 6.0 0.3 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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