Contacts of the strand formed by residues 327 - 341 (chain A) in PDB entry 4CAA
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 LEU 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 4.6 9.2 - - + -
181A MET* 3.7 30.1 - - + -
182A MET* 4.8 6.3 - - + -
316A ALA* 4.0 10.4 - - - +
318A LEU* 4.2 23.3 + - + +
321A ILE* 3.8 39.5 - - + -
322A THR* 4.5 11.4 - - + +
325A ARG 3.8 0.6 - - - -
326A ASN* 1.3 99.4 - - - +
328A ALA* 1.3 64.4 + - - +
355A ILE* 3.7 14.4 - - + -
356A THR 3.4 13.9 - - - +
358A LEU* 3.6 14.2 - - - +
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ALA 4.0 3.6 - - - +
312A PHE 5.0 2.2 - - - +
313A THR 3.7 24.7 - - - +
316A ALA* 4.0 6.7 - - + -
318A LEU* 4.4 4.0 - - - -
327A LEU* 1.3 78.0 - - - +
329A VAL* 1.3 67.0 + - - +
355A ILE* 3.5 4.9 - - - +
356A THR* 3.0 35.7 + - - +
357A LEU 5.2 1.6 - - - +
358A LEU* 4.2 13.9 - - + -
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 4.0 30.7 - - + -
311A ALA* 2.9 33.6 + - + +
312A PHE* 3.6 48.2 - - + +
318A LEU* 4.6 7.2 - - + -
328A ALA* 1.3 72.7 - - - +
330A SER* 1.3 65.2 + - - +
331A GLN 3.9 7.0 - - - +
332A VAL* 4.2 17.0 - - + -
353A VAL* 4.4 12.6 - - + -
354A LYS 4.4 2.2 - - - -
355A ILE* 4.7 3.8 - - + +
356A THR* 5.4 0.4 - - - -
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Residues in contact with SER 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ASP* 4.9 6.9 + - - +
300A ASN* 3.2 12.5 + - - -
312A PHE* 4.2 3.5 - - - -
328A ALA 3.5 0.6 + - - -
329A VAL* 1.3 76.0 - - - +
331A GLN* 1.3 70.7 + - - +
354A LYS* 2.8 30.9 + - - +
356A THR* 3.4 26.5 - - - +
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Residues in contact with GLN 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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175A ASP* 5.9 1.6 - - - +
298A ASN* 3.0 17.3 - - - +
300A ASN* 3.0 21.8 - - - +
329A VAL* 3.8 3.4 - - - +
330A SER* 1.3 88.2 + - - +
332A VAL* 1.3 66.2 + - - +
333A VAL* 2.9 31.9 - - - +
352A ALA 4.0 0.5 - - - +
353A VAL* 3.9 0.2 - - - -
354A LYS* 3.1 60.3 + - + +
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 5.4 1.3 - - + -
61A LEU* 4.5 9.0 - - + -
64A LEU* 5.9 0.2 - - + -
298A ASN* 3.7 2.4 - - - -
299A LEU* 2.8 54.4 + - + +
300A ASN* 2.9 9.7 + - - +
303A LEU* 4.4 23.8 - - + -
312A PHE* 5.1 1.8 - - + -
329A VAL* 4.2 11.2 - - + -
331A GLN* 1.3 78.6 - - - +
333A VAL* 1.3 62.7 + - - +
351A THR* 4.2 11.0 - - + -
352A ALA 3.6 7.9 - - - +
353A VAL* 3.7 31.2 - - + -
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Residues in contact with VAL 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 4.5 22.7 - - + +
173A ILE* 5.0 0.7 - - + -
297A TYR 3.3 13.0 - - - +
298A ASN* 4.4 5.6 - - + +
299A LEU* 5.0 0.2 - - - -
331A GLN* 2.9 34.5 - - - +
332A VAL* 1.3 75.4 - - - +
334A HIS* 1.3 64.4 + - - +
351A THR* 3.3 19.6 - - - +
352A ALA* 3.3 25.5 + - + +
354A LYS* 4.1 20.9 - - - +
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Residues in contact with HIS 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 3.8 15.6 - - + +
53A SER 3.4 34.9 + - - -
56A SER* 4.3 2.7 - - - -
57A ILE* 3.9 16.8 - - + +
172A LEU* 4.4 2.7 - - - +
296A ASP* 3.2 2.8 - - - -
297A TYR* 2.7 50.1 + + + +
299A LEU* 4.0 19.5 - - + -
333A VAL* 1.3 78.5 - - - +
335A LYS* 1.3 64.3 + - - +
336A ALA* 4.3 0.2 - - - +
349A ALA* 3.8 23.0 - - + +
350A ALA 2.9 16.4 + - - -
351A THR* 2.5 27.0 + - + +
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Residues in contact with LYS 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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168A LYS 4.9 1.3 - - - -
169A ILE* 3.7 29.5 - - + +
170A THR* 3.7 31.9 - - - +
171A ASP 4.5 8.3 - - - +
172A LEU* 3.8 16.2 - - + +
294A SER* 2.9 28.9 + - - -
295A ARG 3.8 6.9 + - - +
296A ASP* 4.1 20.6 + - + +
334A HIS* 1.3 76.5 - - - +
336A ALA* 1.3 65.5 + - - +
337A VAL* 4.4 5.0 - - - +
349A ALA* 3.2 2.8 - - - +
350A ALA 2.9 32.4 + - - +
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Residues in contact with ALA 336 (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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51A ILE* 3.6 31.4 - - + +
52A PHE* 3.9 13.2 - - - -
169A ILE* 4.0 1.3 - - - -
294A SER* 3.4 1.9 + - - -
295A ARG 3.0 30.0 + - - +
334A HIS* 4.3 2.9 - - + +
335A LYS* 1.3 77.9 - - - +
337A VAL* 1.3 70.3 + - - +
348A SER 3.4 6.5 - - - +
349A ALA* 3.8 15.5 - - + +
384B PHE* 5.6 0.7 - - + -
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 4.5 4.3 - - - +
168A LYS* 3.8 40.2 - - + +
169A ILE* 3.7 17.7 - - + -
292A SER* 4.8 2.5 - - - +
293A ILE 3.6 9.2 - - - +
294A SER* 3.8 19.1 - - - +
335A LYS* 4.4 4.9 - - - +
336A ALA* 1.3 79.7 - - - +
338A LEU* 1.3 65.2 + - - +
339A ASP* 4.1 13.2 - - - +
347A ALA* 3.2 5.4 - - - +
348A SER 2.8 38.2 + - - +
384B PHE* 5.0 0.2 - - - -
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Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 3.8 18.2 - - + -
291A PHE* 3.6 28.9 - - + +
292A SER* 3.3 6.8 + - - -
293A ILE* 3.0 36.4 + - + +
337A VAL* 1.3 76.1 - - - +
339A ASP* 1.3 65.7 + - - +
340A VAL* 4.2 10.8 - - + -
346A GLU 3.7 4.3 - - - +
347A ALA* 3.8 21.5 - - + -
372B MET* 4.3 16.2 - - + -
374B ILE* 4.1 17.0 - - + -
384B PHE* 5.1 1.8 - - + -
386B SER* 3.9 27.4 - - - +
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Residues in contact with ASP 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LYS* 3.1 31.3 + - - -
291A PHE 3.7 4.5 - - - -
292A SER* 2.6 29.1 + - - -
337A VAL* 4.1 5.2 - - - +
338A LEU* 1.3 75.3 - - - +
340A VAL* 1.3 63.4 + - - +
341A PHE* 3.2 21.7 - - + -
344A GLY 3.1 14.7 - - - +
345A ARG* 3.2 23.7 + - + +
346A GLU* 2.8 19.6 + - - +
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TRP* 4.8 9.6 - - + -
221A MET* 4.0 14.4 - - + -
244A TYR* 5.6 0.7 - - - +
288A LEU* 4.0 13.2 - - + -
289A PRO 3.8 9.2 - - - +
290A LYS* 3.4 5.4 - - - -
291A PHE* 2.7 73.3 + - + +
338A LEU* 4.2 7.1 - - + -
339A ASP* 1.3 73.7 - - - +
341A PHE* 1.3 62.7 + - - +
344A GLY 3.7 4.0 - - - +
372B MET* 3.9 26.2 - - + -
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Residues in contact with PHE 341 (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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194A TRP* 3.2 10.6 + - - -
221A MET* 3.7 10.0 - - - +
290A LYS* 3.4 32.1 - - + -
291A PHE* 4.2 6.7 - - - -
292A SER* 4.2 17.5 - - - -
339A ASP* 3.2 28.5 - - + -
340A VAL* 1.3 75.5 - - - +
342A GLU* 1.3 59.0 + - - +
343A GLU* 3.0 11.2 - - - +
344A GLY 2.7 30.3 + - - -
345A ARG* 3.2 53.6 - - + -
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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
------------------------------------------------------------
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