Contacts of the strand formed by residues 318 - 331 (chain B) in PDB entry 5AZS
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 ARG 318 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B PHE* 3.9 36.7 - - + -
303B GLY* 3.6 8.5 - - - +
304B THR* 4.7 4.3 - - + +
314B ASP 5.1 0.2 + - - -
316B GLY* 3.4 6.0 - - - +
317B SER* 1.3 75.6 - - - +
319B SER* 1.3 59.2 + - - +
320B TRP* 4.3 12.2 - - + +
93C ARG* 3.4 48.9 - - - +
95C PRO* 4.5 6.1 - - - +
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Residues in contact with SER 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLN* 5.0 4.7 + - - -
301B SER* 4.7 2.1 + - - -
302B PHE* 3.8 2.1 + - - -
303B GLY 2.7 34.2 + - - +
304B THR 4.6 0.2 - - - -
305B SER* 3.0 33.2 + - - -
317B SER 3.3 2.9 + - - -
318B ARG* 1.3 74.7 - - - +
320B TRP* 1.3 61.3 + - - +
93C ARG 3.1 18.8 + - - -
94C GLN* 4.3 8.0 + - - +
95C PRO* 4.2 4.9 - - - -
98C LEU* 5.2 0.5 - - - +
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Residues in contact with TRP 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B SER* 3.1 19.7 - - - +
302B PHE* 3.8 29.4 - + + -
318B ARG* 4.3 10.1 - - - +
319B SER* 1.3 77.3 + - - +
321B SER* 1.3 73.7 + - - +
322B PHE* 4.3 7.0 - - + -
91C ARG* 3.6 51.8 - - + -
92C GLN* 3.4 4.9 - - - +
93C ARG* 3.0 72.2 + - + +
106C VAL* 4.1 22.7 - - + -
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Residues in contact with SER 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B GLY* 3.2 7.0 - - - -
301B SER* 3.0 44.0 + - - +
320B TRP* 1.3 79.6 - - - +
322B PHE* 1.3 59.1 + - - +
323B LEU* 3.0 28.7 - - - +
91C ARG 3.4 6.3 - - - -
92C GLN* 4.0 16.5 + - - +
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Residues in contact with PHE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 6.3 3.1 - - + -
298B LEU* 4.6 22.7 - - + -
299B THR 3.9 7.4 - - - -
300B GLY* 5.6 1.6 - - - -
320B TRP* 4.7 8.5 - - + -
321B SER* 1.3 75.3 + - - +
323B LEU* 1.3 62.6 + - - +
324B PRO* 3.6 32.7 - - + +
90C ASN* 3.5 1.6 - - - -
91C ARG* 2.7 56.1 + - + +
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B SER 3.5 1.7 - - - +
298B LEU* 3.5 4.2 - - - -
299B THR* 3.0 53.2 + - - +
300B GLY* 6.1 0.2 - - - -
321B SER* 3.0 29.8 - - - +
322B PHE* 1.3 78.8 - - - +
324B PRO* 1.3 62.7 - - - +
325B THR* 4.6 7.0 + - - +
89C GLY 3.4 6.1 - - - +
90C ASN* 3.7 25.6 - - + -
91C ARG 4.5 0.7 - - - +
92C GLN* 5.5 1.6 - - - +
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Residues in contact with PRO 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ILE* 5.4 4.5 - - + -
297B SER 3.5 5.2 - - - +
298B LEU* 4.6 13.5 - - + -
322B PHE* 3.6 38.4 - - + +
323B LEU* 1.3 83.3 - - - +
325B THR* 1.3 61.9 + - - +
87C ALA 3.9 1.9 - - - +
88C THR* 3.8 0.5 - - - -
89C GLY* 2.9 45.2 + - - +
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Residues in contact with THR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ARG 3.5 2.4 - - - +
296B ILE* 3.5 3.8 - - - +
297B SER* 2.7 55.7 + - - +
323B LEU* 4.6 8.7 + - - +
324B PRO* 1.3 75.4 + - - +
326B LEU* 1.3 63.7 + - - +
327B THR* 4.1 14.8 + - - +
86C ALA* 5.5 1.3 - - + -
87C ALA 3.7 2.7 - - - -
88C THR* 3.9 27.1 - - + +
89C GLY 5.1 0.7 + - - -
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B PRO* 3.5 33.2 - - + -
295B ARG 3.6 2.0 - - - +
296B ILE* 3.6 30.1 - - + +
324B PRO 4.3 0.2 - - - -
325B THR* 1.3 73.3 - - - +
327B THR* 1.3 65.1 + - - +
328B LEU* 5.4 2.0 - - + +
86C ALA* 3.1 9.0 - - - +
87C ALA* 2.9 52.6 + - + +
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Residues in contact with THR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B PRO* 3.2 4.2 - - - +
295B ARG* 2.9 40.4 + - - +
325B THR* 4.1 13.5 + - - +
326B LEU* 1.3 78.8 + - - +
328B LEU* 1.3 61.6 + - - +
329B PRO* 4.7 2.3 - - + +
84C ASN* 3.4 30.7 - - - +
85C ALA 3.6 8.5 - - - +
86C ALA* 4.4 7.7 - - + +
115C ALA* 6.2 0.4 - - + -
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B PHE 4.0 13.0 - - - +
293B PHE* 4.5 0.4 - - - -
294B PRO* 3.5 39.5 - - + -
326B LEU* 5.4 1.5 - - + +
327B THR* 1.3 75.2 - - - +
329B PRO* 1.4 71.1 - - + +
330B ILE* 3.7 16.1 + - + +
84C ASN* 3.1 3.6 - - - +
85C ALA* 2.9 42.3 + - + +
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Residues in contact with PRO 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B ALA 4.6 4.5 - - - +
292B PHE* 3.8 24.8 - - + +
293B PHE 4.8 2.7 - - - +
327B THR* 4.7 1.8 - - + +
328B LEU* 1.4 87.4 - - + +
330B ILE* 1.3 65.7 + - - +
331B PHE 4.7 7.2 - - - +
332B ASP* 4.6 14.1 - - + +
336B ASN* 4.3 19.3 - - - +
84C ASN* 3.3 19.1 - - + +
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Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B LEU* 3.9 11.7 - - + +
329B PRO* 1.3 75.7 - - - +
331B PHE* 1.3 102.9 + - + +
83C LEU* 3.3 17.9 + - + +
84C ASN* 4.1 2.2 - - - -
85C ALA* 3.3 39.5 - - + +
114C LEU* 4.4 10.8 - - + -
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Residues in contact with PHE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B PRO* 4.7 4.6 - - - +
330B ILE* 1.3 111.5 - - + +
332B ASP* 1.3 69.8 + - - +
81C PRO 5.7 0.7 - - - +
82C GLY* 3.5 1.6 - - - -
83C LEU* 2.9 46.3 + - + +
84C ASN* 5.2 0.3 - - - +
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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