Contacts of the strand formed by residues 348 - 355 (chain L) in PDB entry 6AHU
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 ASP 348 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5H ALA 3.6 23.3 + - - +
6H ALA* 4.9 2.1 - - - -
7H THR 5.7 0.2 + - - -
19L LYS* 6.4 0.9 - - + -
20L SER 3.1 17.5 - - - +
21L ASN* 3.9 8.3 - - - +
22L PHE* 4.3 1.3 - - - -
224L SER* 3.3 24.4 + - - +
343L ILE* 3.6 0.5 - - - -
344L PHE* 2.7 36.8 + - + -
346L ASN* 3.2 35.3 + - - +
347L GLN* 1.3 84.4 - - - +
349L TYR* 1.3 60.1 + - - +
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Residues in contact with TYR 349 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A A 3.3 18.6 + - - -
18L GLU 5.2 0.7 - - - -
19L LYS* 3.4 6.4 - - - +
20L SER* 3.3 49.2 + - - -
21L ASN 3.7 16.8 - - - -
22L PHE* 3.5 38.8 - + + -
27L SER* 2.9 22.0 + - - -
29L HIS* 3.3 23.7 + - + +
341L PHE* 3.8 25.8 - + + -
342L VAL 3.3 8.7 - - - +
343L ILE* 4.3 7.0 - - + -
344L PHE* 4.6 0.2 - - - -
348L ASP* 1.3 77.2 - - - +
350L TRP* 1.3 71.5 + - - +
351L LEU* 4.4 14.8 - - + -
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Residues in contact with TRP 350 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L CYS* 5.0 2.0 - - - -
18L GLU 3.4 2.9 - - - +
19L LYS* 3.8 13.0 - - + -
222L LEU* 3.7 36.1 - - + -
223L GLN 3.2 26.7 - - - -
224L SER* 3.5 18.8 + - - -
226L GLU 3.9 12.6 - - - -
227L LEU* 3.7 17.6 - - + +
235L CYS 4.8 3.1 - - - -
237L ALA* 3.7 32.5 - - + -
240L LEU* 4.8 4.7 - - + -
340L ASN 3.1 15.2 - - - +
341L PHE* 3.3 2.3 - - - -
342L VAL* 3.2 41.7 + - + +
344L PHE* 3.6 25.0 - + - -
349L TYR* 1.3 84.7 - - - +
351L LEU* 1.3 60.7 + - - +
352L GLN* 3.8 16.4 + - + +
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Residues in contact with LEU 351 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A A 5.4 4.7 - - - +
16L VAL 3.0 15.8 - - - +
17L CYS* 3.4 0.3 - - - -
18L GLU* 2.6 56.9 + - + +
28L ARG 5.7 2.2 - - - +
29L HIS* 6.3 1.8 - - - -
32L LEU* 3.7 34.3 - - + -
339L TYR* 4.7 3.8 - - + -
340L ASN 3.5 13.5 - - - +
341L PHE* 3.9 26.0 - - + -
349L TYR* 4.2 15.2 + - + -
350L TRP* 1.3 70.5 - - - +
352L GLN* 1.3 59.8 + - - +
353L MET* 4.0 21.3 - - + +
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Residues in contact with GLN 352 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15L LEU* 5.7 2.7 - - + -
16L VAL 3.7 4.3 - - - -
17L CYS* 4.2 15.5 - - + -
237L ALA* 2.7 44.1 + - - +
240L LEU* 4.8 3.8 - - - +
241L PHE* 3.2 41.4 + - + +
338L LEU 4.5 0.2 - - - -
339L TYR* 3.3 4.2 - - - -
340L ASN* 3.0 46.6 + - + +
342L VAL* 4.9 6.2 - - - +
350L TRP* 3.8 15.7 + - + +
351L LEU* 1.3 75.2 - - - +
353L MET* 1.3 62.6 + - - +
354L ALA 3.9 1.0 + - - -
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Residues in contact with MET 353 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14L LEU 4.0 0.2 - - - +
15L LEU* 3.5 10.2 - - - +
16L VAL* 3.2 45.8 + - + +
18L GLU* 4.3 7.2 - - - +
32L LEU* 3.7 28.3 - - + -
324L TRP* 4.2 19.7 - - + -
338L LEU 3.3 5.4 - - - +
339L TYR* 4.1 14.6 - - + +
351L LEU* 4.0 28.3 - - + -
352L GLN* 1.3 73.7 - - - +
354L ALA* 1.3 61.3 - - - +
355L VAL* 3.8 2.8 + - - +
361L CYS* 3.7 18.8 - - - -
362L PRO* 3.5 24.9 - - - +
363L PRO 4.8 0.2 - - - -
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Residues in contact with ALA 354 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H PHE* 5.6 3.4 - - + -
15L LEU* 3.7 9.9 - - + -
241L PHE* 4.0 22.4 - - + -
324L TRP* 3.7 8.7 - - - -
336L GLU 4.2 6.7 - - - +
337L HIS* 3.5 7.3 - - - -
338L LEU* 2.5 50.3 + - + +
352L GLN 3.9 1.2 + - - -
353L MET* 1.3 71.7 - - - +
355L VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 355 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L HIS* 4.0 8.1 + - - +
14L LEU* 3.2 52.1 + - + +
15L LEU* 4.6 0.6 - - - +
16L VAL* 5.6 1.3 - - + -
324L TRP* 4.5 4.9 - - + -
336L GLU 4.1 2.7 - - - -
353L MET 4.3 6.7 - - - +
354L ALA* 1.3 77.2 - - - +
356L GLY* 1.3 72.7 + - - +
359L ASP* 3.3 40.2 - - + +
360L HIS 4.2 5.4 - - - +
361L CYS* 3.8 29.6 - - + -
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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