Contacts of the strand formed by residues 292 - 299 (chain A) in PDB entry 5HKE
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 ASN 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A THR* 3.8 4.2 - - - -
289A THR* 3.0 38.8 + - + +
290A TYR 3.4 0.2 - - - -
291A GLU* 1.3 76.5 - - - +
293A ARG* 1.3 65.6 + - - +
294A GLN* 3.3 26.2 + - - +
296A VAL* 4.7 10.3 - - - +
315A GLU* 4.0 19.5 + - - +
317A LYS 3.2 20.1 + - - +
318A GLN* 3.4 1.7 - - - +
319A ILE* 2.9 39.0 + - - +
321B ASN* 6.1 0.4 - - - +
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Residues in contact with ARG 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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250A HIS* 6.1 2.8 - - - -
288A THR* 3.6 1.3 - - - +
289A THR 4.9 0.2 - - - -
290A TYR 5.5 1.3 + - - +
292A ASN* 1.3 71.8 - - - +
294A GLN* 1.3 63.9 + - - +
318A GLN* 2.7 24.3 + - - +
246B THR* 6.3 0.2 - - + -
249B PHE* 4.1 31.8 + - - +
250B HIS* 6.1 6.4 + - + +
256B GLU* 5.7 3.2 + - - -
288B THR* 3.5 24.5 + - - +
289B THR 5.3 1.8 + - - -
293B ARG* 2.9 97.9 + - - +
294B GLN* 4.9 1.1 - - - -
295B ILE* 3.7 25.1 - - + -
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Residues in contact with GLN 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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287A TYR 3.9 4.5 - - - +
288A THR* 4.3 1.1 - - - -
292A ASN* 3.3 29.7 + - - +
293A ARG* 1.3 79.9 - - - +
295A ILE* 1.3 70.2 + - - +
296A VAL* 3.5 5.9 + - - +
318A GLN* 4.4 0.6 + - - -
319A ILE* 3.7 19.2 + - - +
293B ARG* 4.8 0.2 - - - -
294B GLN* 3.5 50.8 + - + +
319B ILE* 2.9 36.8 + - - +
320B ILE 4.0 0.6 - - - -
321B ASN* 3.7 27.2 + - + +
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Residues in contact with ILE 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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245A ILE* 4.5 7.0 - - + +
249A PHE* 3.8 24.2 - - + -
286A TYR* 3.8 38.1 - - + -
287A TYR 3.4 8.5 - - - +
288A THR* 3.7 18.2 - - + -
293A ARG 3.4 0.4 + - - -
294A GLN* 1.3 76.4 - - - +
296A VAL* 1.3 58.1 + - - +
293B ARG* 3.8 12.0 - - - +
318B GLN* 3.7 38.3 + - + +
319B ILE 4.7 1.8 + - - +
320B ILE* 3.4 16.4 - - + -
321B ASN* 2.8 30.8 + - - +
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Residues in contact with VAL 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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285A LEU 3.6 0.7 - - - +
286A TYR* 3.1 4.0 - - - -
287A TYR* 2.8 79.8 + - + +
292A ASN* 4.7 11.4 - - - +
294A GLN* 3.9 9.6 - - + +
295A ILE* 1.3 77.5 - - - +
297A ALA* 1.4 62.2 + - - +
315A GLU* 6.0 4.3 - - + -
321B ASN* 3.3 27.6 - - + +
323B LEU* 3.8 26.5 - - + -
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Residues in contact with ALA 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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284A THR* 4.4 6.1 - - + -
285A LEU 3.2 5.2 - - - +
286A TYR* 3.7 21.1 - - + -
296A VAL* 1.4 75.1 - - - +
298A VAL* 1.3 63.3 + - - +
320B ILE* 3.6 21.3 - - + +
321B ASN 2.9 7.7 + - - +
322B LYS* 3.8 12.5 - - + -
323B LEU* 2.9 30.7 + - - +
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Residues in contact with VAL 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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28A VAL* 3.9 27.1 - - + -
30A ILE* 4.4 2.0 - - + -
52A ILE* 3.7 11.4 - - + +
284A THR* 3.6 1.1 - - - -
285A LEU* 2.8 52.1 + - + +
287A TYR* 4.9 3.1 - - + -
297A ALA* 1.3 78.3 - - - +
299A THR* 1.3 73.6 + - - +
312A TYR* 4.0 31.6 - - + +
323B LEU* 4.4 21.8 - - + -
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Residues in contact with THR 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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30A ILE* 4.2 6.4 - - - +
52A ILE* 4.1 2.7 - - - +
282A ASN 3.8 8.5 - - - +
283A LYS* 3.5 13.0 - - + +
284A THR* 2.9 24.6 + - - +
298A VAL* 1.3 84.1 - - - +
300A LEU* 1.3 77.8 + - - +
323B LEU 5.8 0.8 - - - -
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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