Contacts of the strand formed by residues 283 - 291 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D ASP* 3.8 17.7 - - - +
149D THR* 3.4 22.4 - - + -
150D ALA* 3.6 28.5 - - + -
153D GLN* 3.4 29.9 - - + +
160D ALA* 3.2 15.7 + - + -
163D VAL* 3.0 30.0 + - - +
274D SER* 3.7 9.4 - - - +
275D ASN* 3.5 22.0 - - - -
276D ARG* 3.7 35.4 - - + -
282D MET* 1.3 82.0 - - + +
284D LEU* 1.3 63.2 + - - +
318D ILE* 3.3 24.1 - - - +
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Residues in contact with LEU 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ASP* 3.4 14.6 - - - -
196D GLY 4.0 4.3 - - - +
273D VAL 3.6 0.5 - - - +
274D SER* 3.8 2.6 + - - -
275D ASN* 3.0 28.0 + - - +
277D ARG* 4.7 4.9 - - + -
280D MET* 4.1 22.4 - - + -
282D MET 4.1 7.0 - - - +
283D TYR* 1.3 78.7 - - - +
285D SER* 1.3 73.5 + - - +
286D TYR* 3.6 13.1 + - + -
311D LEU* 3.9 26.2 - - + +
314D SER* 4.7 2.7 - - - -
315D ARG* 3.5 37.9 - - + +
318D ILE* 3.7 11.2 - - + -
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Residues in contact with SER 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D ASP* 3.9 1.1 + - - -
167D GLY* 3.2 12.3 - - - -
168D THR* 2.7 49.1 + - - +
195D LEU* 3.6 7.4 - - - +
196D GLY* 2.9 38.9 + - - -
272D VAL* 4.2 4.3 - - - -
273D VAL 3.5 6.9 - - - -
274D SER* 3.8 5.5 + - - -
284D LEU* 1.3 72.5 - - - +
286D TYR* 1.3 63.6 + - - +
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Residues in contact with TYR 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D LEU* 4.0 11.2 - - + -
272D VAL* 4.0 5.0 - - - +
273D VAL 3.5 7.1 + - - +
275D ASN* 2.8 24.8 + - - +
277D ARG* 3.2 54.2 + - - -
284D LEU* 3.6 7.0 + - + -
285D SER* 1.3 74.7 - - - +
287D PRO* 1.3 79.4 - - + +
299D THR* 3.2 18.6 - - - -
300D THR* 4.0 3.5 - - - +
301D LEU* 3.1 39.3 + - + +
303D LEU* 4.1 13.6 - - + +
311D LEU* 3.8 32.1 - - + -
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Residues in contact with PRO 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D TYR* 3.8 34.5 - - + -
195D LEU* 3.5 20.2 - - + -
270D GLU* 4.2 8.7 - - + +
271D LEU 3.3 11.4 - - - +
272D VAL* 3.7 9.8 - - + -
275D ASN* 4.9 0.9 + - - +
277D ARG* 4.6 1.4 + - - -
286D TYR* 1.3 98.7 - - + +
288D ALA* 1.3 60.0 + - - +
299D THR* 3.1 44.1 + - + +
301D LEU* 3.9 12.8 - - + -
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Residues in contact with ALA 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D ALA 3.4 1.9 - - - +
270D GLU* 3.4 1.3 - - - -
271D LEU* 2.9 32.4 + - - +
273D VAL* 4.7 1.3 - - + -
275D ASN* 3.9 23.1 - - - +
286D TYR 4.2 2.0 - - - +
287D PRO* 1.3 77.3 - - - +
289D ILE* 1.3 67.1 + - - +
290D ILE* 3.6 10.9 + - + +
295D VAL* 3.9 12.8 - - + -
297D ALA 3.5 12.8 - - - +
298D GLU* 4.5 2.5 - - - +
299D THR* 4.0 5.6 - - - +
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Residues in contact with ILE 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ASP 4.7 2.5 - - - +
185C LEU* 3.7 24.2 - - + -
212C MET* 3.5 28.7 - - + -
268D HIS* 3.5 38.6 - - + +
269D ALA 3.6 1.6 - - - -
270D GLU* 3.8 20.6 - - + -
288D ALA* 1.3 74.8 - - - +
290D ILE* 1.3 56.6 + - - +
295D VAL* 3.5 2.8 - - - -
296D LEU* 2.7 42.1 + - + +
297D ALA* 2.8 28.9 + - + +
299D THR* 4.0 13.0 - - + -
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Residues in contact with ILE 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ILE* 4.5 7.4 - - + -
259D ILE* 4.5 8.1 - - + +
262D ALA* 4.2 15.1 - - + +
263D VAL* 3.9 27.1 - - + -
268D HIS* 2.9 23.7 + - - -
269D ALA* 2.9 19.8 + - - +
271D LEU* 4.0 24.2 - - + -
273D VAL* 4.1 20.9 - - + -
288D ALA 4.0 10.5 - - - +
289D ILE* 1.3 80.1 - - - +
291D GLY* 1.3 61.0 + - - +
294D GLY 3.4 5.6 - - - +
295D VAL* 3.9 25.8 - - + -
296D LEU* 4.3 0.4 - - - -
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Residues in contact with GLY 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D ALA 4.0 6.3 - - - -
263D VAL* 3.5 19.8 - - - +
266D ASP* 3.5 13.2 - - - -
268D HIS 4.2 0.9 - - - -
290D ILE* 1.3 73.9 - - - +
292D ARG* 1.3 59.6 + - - -
293D ASP 3.2 2.9 - - - -
294D GLY* 2.8 26.7 + - - +
296D LEU* 3.6 14.2 - - - +
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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