Contacts of the strand formed by residues 303 - 308 (chain D) in PDB entry 3BUW
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 TRP 303 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246D ARG 5.7 0.4 - - - -
247D LEU* 2.9 44.4 + - + +
248D PHE* 3.6 39.0 - + - -
261D LEU* 5.1 0.4 - - + -
268D TYR* 3.7 25.6 - + - -
293D PHE* 3.7 27.1 - + - -
294D ARG 3.4 26.9 - - - -
295D LEU* 4.0 8.3 - - + -
296D SER* 4.6 0.2 - - - -
301D GLY 5.3 0.4 - - - -
302D GLN* 1.3 75.8 - - - +
304D ALA* 1.3 60.3 + - - +
305D ILE* 4.5 2.9 - - + -
318D ILE* 3.3 15.0 - - - +
319D PRO* 3.2 31.0 - - + +
324D LEU* 3.5 50.1 - - + +
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Residues in contact with ALA 304 (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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323C PTR 4.0 16.6 - - + -
277D VAL* 5.9 0.5 - - - +
293D PHE* 3.4 2.8 - - - -
294D ARG* 2.9 72.3 + - - +
296D SER* 4.3 9.9 - - - -
302D GLN 4.1 0.4 + - - -
303D TRP* 1.3 74.3 - - - +
305D ILE* 1.3 63.2 + - - +
306D GLY 3.9 1.1 + - - -
316D GLN* 4.7 2.6 + - + +
317D THR 3.4 4.5 - - - -
318D ILE* 4.3 0.9 - - + -
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Residues in contact with ILE 305 (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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291D TYR* 4.2 8.3 - - + -
292D ILE 3.6 8.7 - - - +
293D PHE* 3.0 30.1 - - + -
303D TRP* 4.5 2.9 - - + -
304D ALA* 1.3 73.9 - - - +
306D GLY* 1.3 63.6 + - - +
307D TYR* 4.7 2.3 - - - -
315D LEU 3.7 0.9 - - - +
316D GLN* 3.1 3.5 - - - -
317D THR* 2.8 43.5 + - - +
319D PRO* 4.3 17.9 - - + -
324D LEU* 3.6 26.9 - - + -
327D ALA* 5.6 0.9 - - + -
328D LEU* 4.2 6.1 - - + -
337D TYR* 3.5 48.0 - - + +
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Residues in contact with GLY 306 (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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277D VAL* 4.2 12.6 - - - +
281D LEU* 3.6 7.6 - - - +
291D TYR* 3.1 7.0 - - - +
292D ILE 2.8 35.8 + - - -
304D ALA 3.9 1.4 + - - -
305D ILE* 1.3 73.7 - - - +
307D TYR* 1.3 61.9 + - - -
315D LEU 3.2 8.7 - - - -
316D GLN* 3.7 14.5 - - - +
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Residues in contact with TYR 307 (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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324C GLU* 5.6 0.2 - - + -
327C LEU* 5.7 5.5 - - - +
281D LEU* 3.7 6.0 - - - +
290D SER 3.2 11.7 - - - +
291D TYR* 3.8 5.4 - - + -
305D ILE 4.7 3.8 - - - -
306D GLY* 1.3 75.7 - - - +
308D VAL* 1.3 73.7 + - - +
309D THR* 3.8 28.3 + - + +
313D ASN 3.5 1.6 - - - +
314D ILE* 3.4 3.5 - - - -
315D LEU* 2.8 61.7 + - + +
317D THR* 4.7 13.2 - - + -
336D PHE* 3.5 56.8 - + + +
337D TYR* 4.0 20.6 - + + -
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Residues in contact with VAL 308 (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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281D LEU* 4.0 26.2 - - + +
284D PHE 3.7 18.6 - - - +
285D ILE* 3.6 29.4 - - + +
287D LYS 4.0 7.4 - - - +
288D PRO* 3.4 9.4 - - + +
289D GLY 3.0 20.4 + - - -
290D SER* 2.9 25.4 + - - +
307D TYR* 1.3 83.1 - - - +
309D THR* 1.3 73.1 + - - +
312D GLY* 5.0 0.4 - - - -
313D ASN 3.5 6.3 - - - +
314D ILE* 4.4 7.6 - - + -
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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