Contacts of the strand formed by residues 318 - 331 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A PHE* 3.7 37.8 - - + -
303A GLY 3.6 11.7 - - - +
304A THR* 4.3 6.0 - - + +
316A GLY* 3.3 7.5 - - - +
317A SER* 1.3 79.9 + - - +
319A SER* 1.3 62.7 + - - +
320A TRP* 6.1 3.6 - - + -
93B ARG* 3.8 30.1 - - - +
95B PRO* 4.4 8.0 - - - +
104B SER* 6.1 0.2 - - - -
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Residues in contact with SER 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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111A GLN* 5.3 0.2 + - - -
302A PHE* 4.6 1.8 - - - -
303A GLY 2.8 35.3 + - - +
304A THR* 3.6 4.5 + - - -
305A SER* 2.7 39.0 + - - -
318A ARG* 1.3 77.2 - - - +
320A TRP* 1.3 60.9 + - - +
92B GLN* 5.9 0.4 - - - -
93B ARG* 3.4 22.2 - - - -
95B PRO* 3.9 11.0 - - - -
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Residues in contact with TRP 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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301A SER* 3.3 14.1 - - - +
302A PHE* 3.7 26.0 - + + +
318A ARG* 6.2 3.4 - - - -
319A SER* 1.3 79.2 - - - +
321A SER* 1.3 69.0 + - - +
322A PHE* 3.8 15.9 - + + -
91B ARG* 3.4 59.9 - - + -
92B GLN* 3.0 10.9 - - - +
93B ARG* 2.8 64.2 + - + +
106B VAL* 4.6 13.6 - - + +
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Residues in contact with SER 321 (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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300A GLY* 3.4 1.9 - - - -
301A SER* 2.7 54.4 + - - +
320A TRP* 1.3 75.4 - - - +
322A PHE* 1.3 63.5 + - - +
323A LEU* 5.2 3.2 - - - +
90B ASN* 4.4 10.2 + - - -
91B ARG 3.5 10.6 + - - -
92B GLN* 3.8 22.2 + - - +
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Residues in contact with PHE 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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116A LEU* 6.1 2.5 - - + -
298A LEU* 4.9 21.3 - - + -
299A THR 3.7 10.5 - - - -
300A GLY* 4.4 2.9 - - - -
320A TRP* 3.7 15.7 - + + -
321A SER* 1.3 75.6 + - - +
323A LEU* 1.3 61.6 + - - +
324A PRO* 3.5 36.2 - - + +
90B ASN* 3.8 0.9 - - - +
91B ARG* 2.8 50.5 + - + +
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Residues in contact with LEU 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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297A SER 3.9 0.5 - - - +
298A LEU* 3.7 1.5 - - - -
299A THR* 2.9 59.8 + - + +
321A SER* 5.2 3.1 - - - +
322A PHE* 1.3 76.1 - - - +
324A PRO* 1.3 61.3 - - - +
325A THR* 3.9 20.4 + - + +
88B THR* 5.2 5.4 - - - +
89B GLY 3.3 20.6 - - - +
90B ASN* 3.6 28.7 - - + +
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Residues in contact with PRO 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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296A ILE* 5.9 2.0 - - + -
297A SER 3.5 5.8 - - - +
298A LEU* 3.8 21.1 - - + -
322A PHE* 3.5 33.4 - - + +
323A LEU* 1.3 87.8 - - - +
325A THR* 1.3 60.4 + - - +
87B ALA 4.6 0.3 - - - +
89B GLY* 2.9 45.9 + - - +
91B ARG* 5.5 1.1 - - + +
110B TYR* 6.5 1.1 - - + -
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Residues in contact with THR 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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295A ARG 4.1 0.5 - - - +
296A ILE* 3.5 5.0 - - - +
297A SER* 2.9 46.6 + - - +
299A THR* 5.9 0.7 - - - +
323A LEU* 3.9 27.4 - - + +
324A PRO* 1.3 79.7 - - - +
326A LEU* 1.3 60.8 + - - +
327A THR* 5.5 3.2 - - - +
87B ALA 3.7 4.9 - - - -
88B THR* 3.9 24.2 - - + -
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Residues in contact with LEU 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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294A PRO* 4.4 18.4 - - + -
295A ARG 3.6 5.2 - - - +
296A ILE* 3.7 34.1 - - + +
325A THR* 1.3 75.8 - - - +
327A THR* 1.3 73.5 + - - +
328A LEU* 4.7 6.3 - - + +
85B ALA 5.1 0.7 - - - +
86B ALA* 3.7 5.1 - - - +
87B ALA* 2.8 54.3 + - + +
88B THR* 5.0 0.7 - - - +
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Residues in contact with THR 327 (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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294A PRO* 3.3 2.8 - - - +
295A ARG* 2.8 62.9 + - + +
297A SER* 5.7 2.0 - - - +
325A THR* 5.5 4.3 - - - +
326A LEU* 1.3 80.3 - - - +
328A LEU* 1.3 61.4 + - - +
329A PRO* 3.9 4.8 - - + +
84B ASN* 3.6 24.5 + - - +
85B ALA 3.6 10.1 + - - -
86B ALA* 4.6 5.8 - - - +
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Residues in contact with LEU 328 (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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292A PHE 3.9 14.8 - - - +
294A PRO* 3.8 36.6 - - + -
326A LEU* 4.7 5.8 - - + +
327A THR* 1.3 75.5 + - - +
329A PRO* 1.3 74.5 - - - +
330A ILE* 4.0 19.1 - - + -
84B ASN* 3.5 1.1 - - - -
85B ALA* 2.8 47.9 + - + +
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Residues in contact with PRO 329 (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 ALA 3.9 22.9 - - - +
292A PHE* 4.4 8.1 - - - +
293A PHE 4.4 3.8 - - - +
295A ARG* 5.3 0.7 - - + +
327A THR* 3.9 7.2 - - + +
328A LEU* 1.3 100.7 - - + +
330A ILE* 1.3 59.6 + - - +
332A ASP* 4.0 20.4 - - - +
336A ASN* 4.5 12.1 - - - +
84B ASN* 3.8 20.0 - - - +
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Residues in contact with ILE 330 (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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328A LEU* 3.5 19.3 + - + -
329A PRO* 1.3 74.2 - - - +
331A PHE* 1.3 92.0 + - + +
332A ASP 4.4 0.2 + - - -
83B LEU* 3.2 15.3 + - + +
84B ASN 4.2 0.7 - - - -
85B ALA* 3.5 38.6 - - + +
114B LEU* 6.0 1.1 - - + -
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Residues in contact with PHE 331 (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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330A ILE* 1.3 97.7 - - + +
332A ASP* 1.3 74.0 + - - +
81B PRO 5.2 1.6 - - - +
82B GLY* 3.3 5.9 - - - -
83B LEU* 2.8 72.4 + - + +
84B ASN* 4.2 1.6 - - - +
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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