Contacts of the helix formed by residues 336 - 354 (chain B) in PDB entry 1CCW
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 THR 336 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LYS* 5.8 5.6 - - + +
78B LEU* 5.2 0.4 - - - -
329B HIS* 3.8 19.3 + - + +
334B ILE 3.6 1.5 + - - +
335B PRO* 1.3 77.8 - - - +
337B LYS* 1.3 65.6 + - - +
338B GLU* 3.2 18.1 + - - +
339B ALA* 3.5 18.6 + - - +
340B ASN* 3.0 21.7 + - - +
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Residues in contact with LYS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU* 5.2 2.7 - - + +
78B LEU* 3.6 34.7 - - + +
81B TYR* 3.5 46.9 - - + -
82B LEU* 3.9 1.4 - - - +
335B PRO 3.9 0.2 + - - -
336B THR* 1.3 74.0 - - - +
338B GLU* 1.3 88.1 + - - +
340B ASN* 3.8 4.1 - - - +
341B ALA* 3.0 29.6 + - - +
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Residues in contact with GLU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 3.8 21.5 + - - +
336B THR* 3.1 19.8 - - - +
337B LYS* 1.3 111.7 + - - +
339B ALA* 1.3 53.4 + - - +
341B ALA* 3.5 2.8 + - - +
342B ALA* 2.8 32.8 + - - +
345B LYS* 5.6 0.7 + - - -
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Residues in contact with ALA 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B THR* 3.6 4.8 - - - -
328B PRO* 3.5 14.7 - - + +
329B HIS* 3.7 39.7 - - + +
335B PRO* 3.9 6.1 - - + -
336B THR* 3.4 17.1 + - - +
338B GLU* 1.3 72.5 - - - +
340B ASN* 1.3 65.3 - - - +
342B ALA* 3.3 9.2 + - - +
343B GLY 3.1 17.0 + - - -
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Residues in contact with ASN 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PRO* 3.4 19.3 - - - +
66B ARG 2.8 28.0 + - - +
67B ALA* 4.0 3.4 - - - +
78B LEU* 5.4 2.4 - - - +
82B LEU* 3.7 27.9 - - + +
325B VAL* 4.7 2.9 - - - +
327B THR* 3.5 21.0 - - - +
335B PRO* 3.9 14.8 + - + +
336B THR 3.0 17.7 + - - +
337B LYS* 4.5 0.9 - - - -
339B ALA* 1.3 74.7 - - - +
341B ALA* 1.3 65.9 + - - +
343B GLY* 3.1 2.6 + - - -
344B ILE* 2.9 29.9 + - - +
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Residues in contact with ALA 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 3.7 22.0 - - + +
82B LEU* 3.9 2.7 - - + +
85B GLU* 4.1 7.2 - - + -
86B GLY* 3.8 25.4 - - - +
337B LYS 3.0 17.9 + - - +
338B GLU 3.7 3.8 - - - +
340B ASN* 1.3 75.4 - - - +
342B ALA* 1.3 58.2 + - - +
344B ILE* 3.7 4.5 - - - +
345B LYS* 2.8 41.3 + - - +
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Residues in contact with ALA 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B PHE* 3.9 15.7 - - + -
328B PRO* 4.4 3.1 - - + -
338B GLU 2.8 16.3 + - - +
339B ALA* 3.3 13.7 - - - +
340B ASN 3.1 0.4 - - - -
341B ALA* 1.3 77.1 - - - +
343B GLY* 1.3 62.7 + - - +
345B LYS* 4.0 5.1 - - - +
346B ALA* 3.0 22.7 + - - +
302D SER* 3.2 31.2 - - - +
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Residues in contact with GLY 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B PHE* 4.7 0.4 - - - -
308B ILE* 4.2 7.3 - - - +
325B VAL* 3.4 7.4 - - - +
326B LYS 3.6 19.3 - - - -
327B THR* 4.6 0.4 - - - -
328B PRO* 4.3 8.0 - - - +
339B ALA 3.1 13.3 + - - -
340B ASN 3.1 3.3 + - - -
342B ALA* 1.3 76.6 - - - +
344B ILE* 1.3 56.0 + - - +
346B ALA* 3.5 4.0 + - - +
347B THR* 2.6 34.0 + - - -
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Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 4.7 8.5 - - + +
65B PRO* 3.8 33.7 - - + -
82B LEU* 4.0 33.4 - - + +
86B GLY* 3.2 21.1 - - - +
87B GLY 4.2 1.8 - - - -
88B ALA* 3.9 17.3 - - + +
325B VAL* 3.8 17.9 - - + -
340B ASN 2.9 21.6 + - - +
341B ALA* 3.8 5.4 - - - +
343B GLY* 1.3 77.8 - - - +
345B LYS* 1.3 56.9 + - - +
347B THR* 3.3 3.9 + - - -
348B LYS* 2.9 35.2 + - + +
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Residues in contact with LYS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLU* 3.1 37.5 + - - +
86B GLY 3.7 15.5 - - - +
338B GLU 5.7 0.6 + - - -
341B ALA* 2.8 36.5 + - - +
342B ALA* 3.8 8.9 - - - +
344B ILE* 1.3 73.3 - - - +
346B ALA* 1.3 57.2 + - - +
348B LYS* 4.0 4.1 - - - +
349B MET* 3.0 31.6 + - - +
300D ASP* 2.9 33.4 + - - +
302D SER* 4.1 10.0 + - - -
303D LYS* 4.1 27.1 - - + +
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B PHE* 3.7 22.9 - - + -
308B ILE* 4.6 2.7 - - + -
309B VAL* 4.0 16.8 - - + +
342B ALA 3.0 18.1 + - - +
343B GLY 3.8 3.6 - - - +
345B LYS* 1.3 75.7 - - - +
347B THR* 1.3 58.2 + - - +
349B MET* 3.5 3.8 + - - +
350B ALA* 3.1 28.1 + - - +
302D SER 3.5 23.7 + - - +
306D GLY* 3.9 5.9 - - - +
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Residues in contact with THR 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 4.2 6.1 - - + -
292B GLN* 3.5 20.9 + - - +
308B ILE* 3.7 7.5 - - - +
309B VAL* 5.4 0.4 - - - -
312B THR* 3.4 31.2 - - + +
323B VAL* 3.9 19.7 - - + -
325B VAL* 3.9 15.2 - - + +
343B GLY 2.6 22.9 + - - -
344B ILE 3.5 4.9 - - - -
346B ALA* 1.3 75.3 - - - +
348B LYS* 1.3 61.6 + - - +
350B ALA 3.2 2.3 + - - -
351B LEU* 2.9 31.7 + - + +
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Residues in contact with LYS 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 3.8 20.0 - - + -
86B GLY 4.7 1.3 - - - +
87B GLY* 2.7 36.3 + - - +
88B ALA 4.8 0.2 + - - -
89B ASP* 3.0 33.9 + - - +
344B ILE* 2.9 20.7 + - + +
345B LYS* 4.2 3.8 - - - +
347B THR* 1.3 72.9 - - - +
349B MET* 1.3 61.0 + - - +
351B LEU* 3.3 10.6 + - + +
352B ASN* 2.9 49.0 + - - +
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Residues in contact with MET 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LYS 3.0 19.6 + - - +
346B ALA 3.7 4.3 - - - +
348B LYS* 1.3 76.3 - - - +
350B ALA* 1.3 57.1 + - - +
352B ASN* 3.3 2.3 + - - +
353B MET* 2.9 59.7 + - + +
298D PRO* 4.3 2.5 - - + -
303D LYS* 3.3 47.1 - - + +
306D GLY* 4.2 5.2 - - - -
307D VAL* 3.8 15.9 - - + -
473D VAL* 3.4 25.1 - - + +
476D GLY* 3.6 33.2 - - - +
477D ARG 3.9 0.4 - - - +
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Residues in contact with ALA 350 (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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309B VAL* 3.9 14.1 - - + +
312B THR* 3.8 16.8 - - + -
313B THR* 4.9 1.3 - - - +
346B ALA 3.1 14.0 + - - +
347B THR 3.2 7.8 + - - +
349B MET* 1.3 77.0 - - - +
351B LEU* 1.3 62.6 + - - +
353B MET* 3.2 11.5 + - - +
354B LEU* 3.2 23.9 + - + +
306D GLY* 4.5 2.9 - - - +
310D THR* 3.6 26.2 - - + -
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 3.5 52.3 - - + +
63B ALA* 4.4 8.5 - - + +
89B ASP* 5.4 0.2 - - - +
312B THR* 3.5 21.1 - - + +
315B ALA* 5.3 0.2 - - + -
316B ALA* 3.9 20.0 - - + +
323B VAL* 4.1 14.6 - - + -
347B THR* 2.9 24.1 + - + +
348B LYS* 3.6 15.3 - - + +
350B ALA* 1.3 75.1 - - - +
352B ASN* 1.3 62.8 + - - +
354B LEU* 3.1 19.2 + - - +
355B GLU* 3.2 12.3 + - - +
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Residues in contact with ASN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LYS* 2.9 35.5 + - - +
349B MET* 3.8 1.3 - - - +
351B LEU* 1.3 74.9 - - - +
353B MET* 1.3 60.8 + - - +
354B LEU 3.1 6.1 + - - -
355B GLU* 3.6 17.6 + - - +
476D GLY 3.2 28.3 + - - +
477D ARG* 3.7 17.6 + - + +
478D LEU* 3.2 18.2 + - - +
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Residues in contact with MET 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B MET* 2.9 52.2 + - + +
350B ALA* 3.2 8.9 + - - +
352B ASN* 1.3 75.1 - - - +
354B LEU* 1.3 63.9 + - + +
355B GLU 3.6 0.4 - - - -
357B GLN* 3.6 3.6 + - - -
254D GLU* 4.7 13.2 - - - +
256D GLY* 3.9 3.9 - - - +
293D TRP* 5.1 5.4 - - + -
307D VAL* 4.4 19.3 - - + -
310D THR* 4.4 16.4 - - - +
473D VAL* 3.8 27.4 - - + -
477D ARG 4.0 0.2 - - - -
478D LEU* 3.5 55.5 - - + +
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B THR* 3.8 46.7 - - + +
316B ALA* 3.9 19.7 - - + +
317B LEU* 5.1 7.2 - - + -
350B ALA 3.3 18.6 - - - +
351B LEU 3.1 7.0 + - - +
352B ASN 3.1 0.6 - - - -
353B MET* 1.3 85.7 - - + +
355B GLU* 1.3 64.1 + - - +
356B GLY 3.2 0.5 + - - -
357B GLN* 2.9 48.6 + - + +
358B ARG* 5.0 0.7 + - - -
256D GLY 4.5 5.4 - - - +
258D MET* 5.2 8.5 - - + -
310D THR* 4.3 14.6 - - + -
314D ILE* 5.3 4.0 - - + -
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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
------------------------------------------------------------
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