Contacts of the strand formed by residues 303 - 308 (chain A) in PDB entry 5HKZ
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LEU* 3.0 45.1 + - + +
248A PHE* 3.6 40.4 - + - -
261A LEU* 5.2 1.1 - - + -
268A TYR* 3.7 28.0 - + - -
293A PHE* 3.8 23.3 - + - -
294A ARG 3.4 26.9 - - - -
295A LEU* 4.0 8.5 - - + -
296A SER* 4.4 0.7 - - - -
301A GLY 5.2 0.9 - - - -
302A GLN* 1.3 77.0 + - - +
304A ALA* 1.3 61.5 + - - +
305A ILE* 5.2 0.7 - - + -
318A ILE* 3.5 15.9 - - - +
319A PRO* 3.3 27.4 - - + +
324A LEU* 3.5 47.7 - - + +
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Residues in contact with ALA 304 (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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293A PHE* 3.2 3.9 - - - -
294A ARG* 2.8 72.2 + - - +
296A SER* 4.1 8.5 - - - +
303A TRP* 1.3 73.6 - - - +
305A ILE* 1.3 63.2 + - - +
306A GLY 4.0 0.7 + - - -
316A GLN* 4.8 2.2 - - + +
317A THR 3.5 4.5 - - - +
318A ILE* 4.4 0.7 - - + -
55B PTR 3.9 17.9 - - + -
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Residues in contact with ILE 305 (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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291A TYR* 4.3 11.2 - - + -
292A ILE 3.5 9.9 - - - +
293A PHE* 3.9 13.0 - - + -
304A ALA* 1.3 75.7 - - - +
306A GLY* 1.3 65.1 + - - +
307A TYR* 4.0 1.0 - - - -
315A LEU 3.8 0.9 - - - +
316A GLN* 3.2 3.6 - - - -
317A THR* 2.8 44.0 + - + +
319A PRO* 4.0 21.1 - - + -
324A LEU* 3.9 23.8 - - + -
327A ALA* 4.1 7.6 - - + -
328A LEU* 4.3 5.2 - - + -
337A TYR* 3.7 51.4 - - + +
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Residues in contact with GLY 306 (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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277A VAL* 4.1 6.3 - - - +
281A LEU* 3.6 14.5 - - - +
291A TYR* 3.0 5.7 - - - +
292A ILE 2.8 39.3 + - - +
304A ALA 4.0 1.8 + - - -
305A ILE* 1.3 72.7 - - - +
307A TYR* 1.3 61.6 + - - -
315A LEU 3.2 9.0 - - - -
316A GLN* 3.7 14.0 + - - +
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Residues in contact with TYR 307 (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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281A LEU* 3.7 5.2 - - - +
290A SER 3.2 11.0 - - - +
291A TYR* 3.9 10.1 - - + -
305A ILE 4.0 5.4 - - - -
306A GLY* 1.3 78.2 - - - +
308A VAL* 1.3 68.8 + - - +
309A THR* 3.6 22.9 - - + -
313A ASN 3.6 0.3 - - - +
314A ILE* 3.3 3.6 - - - -
315A LEU* 2.9 69.2 + - + +
317A THR* 4.1 20.4 - - + -
336A PHE* 4.2 15.3 - + + +
337A TYR* 3.8 23.8 - + + -
56B THR* 4.8 0.7 + - - -
57B GLU 4.3 5.9 + - - -
59B PRO* 3.5 39.3 - - + +
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Residues in contact with VAL 308 (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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281A LEU* 4.1 26.7 - - + +
284A PHE 3.8 18.6 - - - +
285A ILE* 3.7 29.6 - - + +
287A LYS 4.0 6.7 - - - +
288A PRO* 3.9 7.6 - - + -
289A GLY* 2.9 26.7 + - - -
290A SER* 2.9 27.0 + - - +
307A TYR* 1.3 79.6 - - - +
309A THR* 1.3 72.1 + - - +
312A GLY* 4.6 1.1 - - - -
313A ASN 3.2 9.0 - - - +
314A ILE* 4.3 5.4 - - + -
336A PHE 4.9 0.2 - - - +
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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