Contacts of the strand formed by residues 322 - 335 (chain A) in PDB entry 5C58
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 TYR 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ARG* 2.6 38.0 + - - -
138A HIS* 4.2 5.5 - - - -
139A ALA 4.8 1.9 + - - -
155A GLN 5.3 0.4 - - - -
158A PRO* 3.5 38.1 - - + +
280A ARG* 3.9 14.2 + - + +
281A HIS* 3.9 0.3 - - - -
282A LEU* 3.0 57.0 + - + +
320A THR 3.8 12.8 - - - -
321A HIS* 1.3 78.3 - - - +
323A ARG* 1.3 73.7 + - - +
324A MET* 4.0 24.8 - - + -
351A ALA 3.5 13.9 - - - +
352A SER* 3.5 15.5 - - - +
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Residues in contact with ARG 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 ARG 3.1 11.9 - - - +
281A HIS* 4.0 19.3 - - + +
322A TYR* 1.3 82.5 - - - +
324A MET* 1.3 62.6 + - - +
325A HIS* 3.0 35.5 + - - +
349A GLN* 4.0 17.4 - - - +
350A THR* 3.6 2.4 - - - +
351A ALA* 2.9 58.1 + - + +
376A TYR* 4.5 11.4 + - - +
378A ASP* 5.3 4.8 + - - -
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Residues in contact with MET 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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158A PRO* 5.4 6.7 - - + +
197A TYR* 4.8 2.7 - - + -
198A ILE 3.8 33.7 - - - +
199A ASP* 3.7 18.5 - - + +
278A SER 4.1 0.5 - - - +
279A GLU* 3.9 2.3 - - - -
280A ARG* 3.0 64.2 + - + +
322A TYR* 4.0 16.8 - - + -
323A ARG* 1.3 77.3 - - - +
325A HIS* 1.3 67.9 + - - +
326A SER* 4.2 5.2 - - - +
348A THR* 4.7 6.3 - - - -
349A GLN 3.1 10.5 - - - +
350A THR* 3.8 21.5 - - + +
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Residues in contact with HIS 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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278A SER 3.7 4.0 - - - -
279A GLU* 2.6 37.3 + - - +
281A HIS* 3.6 20.4 - + - -
323A ARG* 3.0 40.8 + - - +
324A MET* 1.3 81.1 - - - +
326A SER* 1.3 61.8 + - - +
327A ARG* 3.9 12.9 + - - +
347A GLN* 3.7 4.9 + - - +
348A THR* 3.7 1.0 - - - -
349A GLN* 2.8 58.0 + - + +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP* 3.2 22.9 + - - +
202A LEU* 3.7 14.4 - - - -
277A ALA* 3.3 0.9 - - - -
278A SER* 3.1 42.3 + - - -
324A MET* 4.5 2.4 - - - +
325A HIS* 1.3 72.9 - - - +
327A ARG* 1.3 78.0 + - - +
346A LEU* 4.8 1.6 - - - -
347A GLN 3.2 7.6 - - - -
348A THR* 3.4 21.1 - - - +
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Residues in contact with ARG 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ALA 3.7 3.4 - - - +
277A ALA* 3.4 21.5 - - - +
278A SER 4.2 3.8 + - - -
279A GLU* 2.5 33.1 + - - +
325A HIS* 3.9 17.5 + - - +
326A SER* 1.3 87.1 + - - +
328A LEU* 1.3 59.9 + - - +
345A TYR* 3.6 7.5 - - + +
346A LEU* 3.4 7.0 - - - +
347A GLN* 3.0 57.9 + - + +
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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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202A LEU* 3.9 24.2 - - + +
230A THR* 4.0 17.7 - - + +
231A VAL* 3.7 31.0 - - + +
274A LEU* 3.8 17.3 - - + -
275A LEU* 3.6 3.3 - - - +
276A ALA* 2.9 43.3 + - + +
327A ARG* 1.3 73.8 - - - +
329A ALA* 1.3 71.2 + - - +
330A LYS* 4.0 17.7 - - + -
344A SER* 5.6 1.1 - - - -
345A TYR* 3.5 11.2 - - - +
346A LEU* 4.0 18.8 - - + -
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Residues in contact with ALA 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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273A ILE* 5.4 1.6 - - + -
274A LEU 3.2 6.1 - - - -
275A LEU* 3.9 17.0 - - + -
328A LEU* 1.3 78.3 - - - +
330A LYS* 1.3 65.1 + - - +
331A VAL* 4.4 2.0 - - + -
343A LEU 4.1 0.4 - - - +
344A SER* 3.2 3.3 - - - -
345A TYR* 2.8 47.7 + - + +
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Residues in contact with LYS 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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178A ASP* 4.1 5.7 + - - -
230A THR* 2.9 27.3 + - - -
231A VAL 2.8 29.8 + - - +
232A SER* 3.2 23.2 + - - +
233A ALA* 5.3 1.3 - - + +
272A ASP* 4.5 3.1 - - - +
273A ILE* 3.3 6.9 - - - +
274A LEU* 2.8 48.8 + - + +
328A LEU* 4.0 15.0 - - + -
329A ALA* 1.3 80.9 - - - +
331A VAL* 1.3 63.8 + - - +
332A GLY 4.0 0.7 + - - -
342A GLN* 3.9 27.2 - - - +
343A LEU 3.3 6.3 - - - +
344A SER* 3.8 16.4 - - - -
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Residues in contact with VAL 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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272A ASP 3.8 9.4 - - - +
273A ILE* 3.6 21.8 - - + -
329A ALA* 5.7 1.8 - - + -
330A LYS* 1.3 72.4 - - - +
332A GLY* 1.3 61.9 + - - +
333A TRP* 3.5 41.5 - - + +
342A GLN* 3.2 6.5 - - - +
343A LEU* 2.9 41.6 + - + +
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Residues in contact with GLY 332 (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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271A GLY* 3.1 3.3 - - - -
272A ASP* 3.0 40.1 + - - +
330A LYS 4.1 0.2 - - - -
331A VAL* 1.3 75.2 - - - +
333A TRP* 1.3 68.7 + - - -
340A ARG* 3.8 26.2 - - - +
341A LEU 3.4 6.5 - - - -
342A GLN* 4.3 0.7 - - - -
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Residues in contact with TRP 333 (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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270A THR 3.6 10.1 - - - +
271A GLY* 5.0 1.8 - - - -
331A VAL* 3.5 36.8 - - + +
332A GLY* 1.3 78.8 + - - -
334A ASN* 1.3 66.2 + - - +
335A LEU* 4.6 13.0 - - + +
340A ARG* 3.2 7.4 - - - +
341A LEU* 2.8 64.7 + - + +
342A GLN* 4.9 0.2 - - - -
343A LEU* 4.2 30.7 - - + -
386A PHE* 5.9 2.0 - + - -
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Residues in contact with ASN 334 (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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268A ASN 5.3 1.8 + - - -
269A GLU* 3.2 29.1 + - - +
270A THR* 2.8 23.1 + - - +
271A GLY* 4.4 1.8 - - - -
272A ASP* 4.3 4.7 + - - +
333A TRP* 1.3 75.6 - - - +
335A LEU* 1.3 70.0 + - - +
339A GLN 3.8 7.9 - - - +
340A ARG* 3.0 31.7 + - - +
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Residues in contact with LEU 335 (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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333A TRP* 4.6 14.4 - - + +
334A ASN* 1.3 90.4 - - - +
336A PRO* 1.4 80.0 - - + +
337A ALA 4.3 2.8 - - - +
338A ASN* 4.5 0.7 - - - -
339A GLN* 3.2 53.5 + - + +
341A LEU* 4.8 22.7 - - + -
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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