Contacts of the strand formed by residues 283 - 291 (chain A) in PDB entry 1HYH
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 TYR 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ASP* 4.0 10.4 - - - +
149A THR* 3.6 21.1 - - + -
150A ALA* 3.6 29.6 - - + -
153A GLN* 3.2 32.8 - - + +
160A ALA* 3.1 14.9 + - + -
163A VAL 2.9 28.9 + - - -
274A SER* 3.8 11.7 - - - +
275A ASN* 3.7 15.7 - - - -
276A ARG* 3.6 43.1 - - + -
282A MET* 1.3 95.3 - - + +
284A LEU* 1.3 61.8 + - - +
318A ILE* 3.3 17.7 - - - +
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Residues in contact with LEU 284 (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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146A ASP* 3.7 9.9 - - - -
196A GLY 4.3 5.2 - - - +
274A SER* 3.8 5.9 + - - -
275A ASN* 3.1 26.0 + - - +
277A ARG* 4.8 1.8 - - - -
280A MET* 4.1 24.7 - - + -
282A MET 3.6 7.2 + - - +
283A TYR* 1.3 77.1 - - - +
285A SER* 1.3 74.4 + - - +
286A TYR* 3.7 11.5 + - + +
311A LEU* 3.7 28.0 - - + +
314A SER* 4.5 2.9 - - - -
315A ARG* 3.6 39.0 - - + +
318A ILE* 3.7 11.2 - - + -
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Residues in contact with SER 285 (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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146A ASP* 4.0 1.1 + - - -
167A GLY* 3.4 11.3 - - - -
168A THR* 2.8 46.5 + - - +
195A LEU* 3.7 7.2 - - - +
196A GLY 3.2 35.0 + - - -
272A VAL* 4.3 2.9 - - - -
273A VAL 3.3 9.9 - - - -
274A SER* 3.7 7.4 + - - -
284A LEU* 1.3 77.5 - - - +
286A TYR* 1.3 64.4 + - - +
311A LEU* 4.2 0.7 - - - +
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Residues in contact with TYR 286 (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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195A LEU* 4.0 5.4 - - + -
272A VAL* 4.0 4.8 - - - +
273A VAL 3.3 6.9 + - - +
275A ASN* 2.8 25.2 + - - +
277A ARG* 3.3 56.5 + - - -
280A MET* 5.8 0.7 - - + -
284A LEU* 3.7 6.2 + - + +
285A SER* 1.3 75.5 - - - +
287A PRO* 1.3 80.5 - - + +
288A ALA 3.5 0.7 + - - -
299A THR* 3.5 17.9 - - - -
300A THR* 4.0 2.6 - - - +
301A LEU* 3.0 44.7 + - + +
303A LEU* 4.4 11.3 - - + +
311A LEU* 3.6 34.8 - - + -
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Residues in contact with PRO 287 (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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193A TYR* 3.8 32.3 - - + -
195A LEU* 3.5 18.4 - - + -
270A GLU* 4.2 13.5 - - + +
271A LEU 3.4 9.6 - - - +
272A VAL* 3.8 9.6 - - + -
275A ASN* 4.9 1.2 + - - +
277A ARG* 4.6 1.4 + - - -
286A TYR* 1.3 100.8 - - + +
288A ALA* 1.3 58.0 + - - +
298A GLU* 4.6 0.3 - - - -
299A THR* 3.0 38.7 + - + +
301A LEU* 3.7 17.9 - - + -
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Residues in contact with ALA 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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269A ALA 3.5 0.9 - - - +
270A GLU* 3.1 5.4 - - - +
271A LEU 3.0 32.5 + - - +
273A VAL* 4.5 1.8 - - + -
275A ASN* 3.9 21.1 - - - +
287A PRO* 1.3 73.7 - - - +
289A ILE* 1.3 67.3 - - - +
290A ILE* 3.9 10.4 + - + +
295A VAL* 3.8 19.1 - - + -
297A ALA 3.6 11.9 - - - +
298A GLU* 4.8 1.3 - - - -
299A THR* 4.1 4.0 - - - +
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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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268A HIS* 3.6 34.3 - - + +
269A ALA 3.5 1.3 - - - -
270A GLU* 3.7 28.7 - - + -
288A ALA* 1.3 73.4 - - - +
290A ILE* 1.3 59.7 + - - +
295A VAL* 3.4 4.9 - - - -
296A LEU* 2.7 40.0 + - + -
297A ALA* 2.8 37.4 + - + +
299A THR* 4.0 11.9 - - + -
184B ASP 4.9 1.3 - - - +
185B LEU* 3.5 28.5 - - + -
212B MET* 4.2 11.4 - - + -
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Residues in contact with ILE 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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164A ILE* 4.5 8.1 - - + -
259A ILE* 4.6 9.4 - - + -
262A ALA* 4.2 15.1 - - + +
263A VAL* 3.8 26.2 - - + -
268A HIS* 2.9 25.6 + - - -
269A ALA* 2.9 22.5 + - - +
271A LEU* 4.1 26.0 - - + -
273A VAL* 4.2 20.6 - - + -
288A ALA* 4.3 7.2 - - + +
289A ILE* 1.3 81.7 - - - +
291A GLY* 1.3 62.7 + - - +
294A GLY 3.4 4.7 - - - +
295A VAL* 4.1 25.1 - - + +
296A LEU* 4.2 1.1 - - - -
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Residues in contact with GLY 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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262A ALA 4.0 7.6 - - - -
263A VAL* 3.7 18.0 - - - +
266A ASP* 3.5 12.8 - - - -
268A HIS 4.1 0.9 - - - -
290A ILE* 1.3 76.7 - - - +
292A ARG* 1.3 60.5 + - - -
293A ASP 3.2 3.4 - - - -
294A GLY* 2.9 27.1 + - - +
296A LEU* 3.7 12.4 - - - +
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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