Contacts of the strand formed by residues 316 - 326 (chain A) in PDB entry 5O67
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 SER 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A TYR* 3.4 2.4 - - - +
289A THR* 2.9 42.1 + - - +
291A ASN* 5.6 0.3 + - - -
314A GLY 4.7 0.7 + - - -
315A ASP* 1.3 80.3 - - - +
317A PHE* 1.3 68.1 + - - +
318A GLN* 2.8 24.1 + - - -
340A LEU* 4.8 2.2 - - - +
341A ILE 3.1 16.4 - - - -
342A GLN* 3.6 21.3 + - - -
343A ARG* 4.7 1.5 - - - +
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Residues in contact with PHE 317 (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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286A VAL* 5.8 5.4 - - + -
287A SER 3.4 13.0 - - - +
288A TYR* 4.1 10.8 - - + -
316A SER* 1.3 79.5 - - - +
318A GLN* 1.3 66.7 + - - +
319A PHE* 4.8 16.4 - + - -
340A LEU* 3.6 0.7 - - - -
341A ILE* 2.9 76.7 + - + +
343A ARG* 4.0 26.5 - - - -
502B LDA 4.8 17.5 - - + -
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Residues in contact with GLN 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 4.6 0.7 - - - +
286A VAL* 3.6 3.3 - - - +
287A SER* 2.8 64.4 + - - +
288A TYR* 3.8 0.2 - - - -
289A THR* 3.3 18.0 + - - -
316A SER* 2.8 39.0 + - - -
317A PHE* 1.3 76.8 - - - +
319A PHE* 1.3 67.6 + - - +
339A ASP 3.5 6.5 - - - +
340A LEU* 3.3 33.7 - - + +
501A LDA 3.5 27.8 - - + -
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Residues in contact with PHE 319 (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 SER 3.2 15.0 - - - +
286A VAL* 4.2 12.3 - - + +
317A PHE* 4.8 15.7 - + - -
318A GLN* 1.3 78.5 - - - +
320A GLY* 1.3 66.9 + - - +
321A VAL* 5.5 5.8 - - + -
338A SER* 3.3 6.9 - - - -
339A ASP* 3.0 46.0 + - + -
341A ILE* 5.2 1.8 - - + -
501A LDA 4.3 6.4 - - - +
398B PHE* 3.9 28.3 - + - -
502B LDA 3.7 32.3 - - + -
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Residues in contact with GLY 320 (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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283A PHE* 6.0 0.7 - - - -
284A GLY* 3.2 1.5 - - - -
285A SER* 3.0 36.1 + - - +
319A PHE* 1.3 81.2 - - - +
321A VAL* 1.3 68.4 + - - +
337A VAL 3.1 14.1 - - - -
338A SER* 4.0 5.4 - - - -
501A LDA 5.5 1.3 - - - -
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PHE* 3.4 13.7 - - - +
284A GLY* 4.2 4.9 - - - -
319A PHE* 5.3 6.9 - - + -
320A GLY* 1.3 79.8 - - - +
322A GLY* 1.3 60.4 + - - +
336A SER* 3.5 4.1 - - - -
337A VAL* 3.0 44.7 + - + +
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Residues in contact with GLY 322 (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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282A LEU* 3.5 5.6 - - - +
283A PHE* 2.9 48.6 + - - +
321A VAL* 1.3 78.9 - - - +
323A VAL* 1.3 61.6 + - - -
335A PHE 3.2 13.2 - - - -
336A SER* 4.0 1.3 - - - -
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Residues in contact with VAL 323 (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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280A ALA* 4.1 10.3 - - + -
281A VAL 3.3 5.2 - - - +
282A LEU* 3.6 26.7 - - + -
283A PHE* 3.8 2.3 - - - -
322A GLY* 1.3 73.7 - - - +
324A ALA* 1.3 62.6 + - - +
325A PHE* 4.0 21.1 - - + -
334A SER* 3.6 1.2 - - - -
335A PHE* 2.8 41.9 + - + +
327B LEU* 5.4 0.2 - - + -
333B MET* 3.7 33.9 - - + -
371B MET* 4.4 19.1 - - + -
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Residues in contact with ALA 324 (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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95A LEU* 4.8 17.3 - - + +
99A ALA* 6.3 0.7 - - + -
279A PRO 3.8 0.2 - - - +
280A ALA* 3.7 1.4 - - - -
281A VAL* 2.8 46.9 + - + +
283A PHE* 4.1 13.2 - - + -
323A VAL* 1.3 74.8 - - - +
325A PHE* 1.3 72.0 + - - +
332A SER* 5.9 0.9 - - - +
333A MET 3.4 12.3 - - - +
334A SER* 4.2 8.1 - - - -
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Residues in contact with PHE 325 (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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95A LEU* 5.8 1.8 - - - -
279A PRO* 3.7 24.0 - - + +
280A ALA* 4.4 11.0 - - - -
281A VAL* 5.4 1.1 - - - -
323A VAL* 4.0 14.4 - - + -
324A ALA* 1.3 84.2 - - - +
326A ALA* 1.3 65.3 + - - +
327A LEU* 3.5 12.0 + - + +
332A SER* 3.3 6.4 - - - -
333A MET* 3.0 39.4 + - + +
335A PHE* 4.1 29.8 - + - -
327B LEU* 3.6 28.7 - - + -
333B MET* 3.9 22.4 - - - -
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Residues in contact with ALA 326 (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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91A SER* 3.7 25.8 - - - +
92A VAL* 4.4 16.6 - - + -
95A LEU* 5.9 1.7 - - + +
279A PRO* 4.6 6.9 + - - +
281A VAL* 5.7 2.6 - - - +
325A PHE* 1.3 70.6 - - - +
327A LEU* 1.3 62.9 + - - +
328A ASN* 4.4 2.4 - - - +
331A MET 3.9 4.7 - - - -
332A SER* 4.3 3.8 - - - -
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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