Contacts of the helix formed by residues 336 - 354 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C LYS* 6.0 3.8 - - + +
78D LEU* 5.1 0.4 - - - -
329D HIS* 3.9 17.5 + - + -
334D ILE 3.6 2.1 + - - +
335D PRO* 1.3 76.3 - - - +
337D LYS* 1.3 65.7 + - - +
338D GLU* 3.4 17.0 + - - +
339D ALA* 2.9 24.4 + - - +
340D ASN* 2.9 22.0 + - - +
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Residues in contact with LYS 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D GLU* 4.5 20.6 + - + +
78D LEU* 3.7 35.3 - - + +
81D TYR* 3.6 47.1 - - + -
82D LEU* 3.8 1.9 - - + +
335D PRO 3.9 0.4 + - - -
336D THR* 1.3 73.8 - - - +
338D GLU* 1.3 88.4 + - - +
340D ASN* 3.5 3.6 + - - +
341D ALA* 2.9 30.7 + - - +
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Residues in contact with GLU 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D TYR* 3.8 21.3 + - - +
336D THR* 3.4 18.3 - - - +
337D LYS* 1.3 111.9 + - - +
339D ALA* 1.3 59.3 + - - +
341D ALA* 3.4 2.7 + - - +
342D ALA* 2.9 27.5 + - - +
345D LYS* 5.8 0.2 - - - -
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Residues in contact with ALA 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D THR* 3.6 3.8 - - - -
328D PRO* 3.5 17.0 - - + +
329D HIS* 3.7 38.8 - - + +
335D PRO* 4.0 5.6 - - + -
336D THR* 2.9 20.2 + - - +
338D GLU* 1.3 75.9 - - - +
340D ASN* 1.3 58.1 + - - +
342D ALA* 3.3 8.4 + - - +
343D GLY 3.0 22.3 + - - -
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Residues in contact with ASN 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D PRO* 3.4 19.1 - - - +
66D ARG 2.9 27.8 + - - +
67D ALA* 4.0 3.6 - - - +
78D LEU* 5.3 2.6 - - + +
82D LEU* 3.6 29.5 - - + +
325D VAL* 4.8 2.6 - - - +
327D THR* 3.5 20.3 - - - +
335D PRO* 3.8 14.7 + - + +
336D THR 2.9 16.4 + - - +
337D LYS* 4.4 0.9 - - - -
339D ALA* 1.3 74.4 - - - +
341D ALA* 1.3 65.6 + - - +
343D GLY* 3.0 3.8 + - - -
344D ILE* 3.0 28.6 + - - +
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Residues in contact with ALA 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D TYR* 3.7 21.8 - - + +
82D LEU* 4.0 2.3 - - + +
85D GLU* 4.4 3.4 - - + -
86D GLY* 3.8 25.7 - - - +
337D LYS 2.9 18.8 + - - +
338D GLU* 3.8 4.9 - - - +
340D ASN* 1.3 74.0 - - - +
342D ALA* 1.3 58.2 + - - +
344D ILE* 3.3 4.9 + - - +
345D LYS* 2.9 42.8 + - - +
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Residues in contact with ALA 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B SER* 3.2 30.0 - - - +
305D PHE* 3.9 14.1 - - + -
328D PRO* 4.5 3.1 - - + -
338D GLU 2.9 16.4 + - - +
339D ALA* 3.4 13.5 - - - +
340D ASN 3.1 0.2 - - - -
341D ALA* 1.3 78.5 - - - +
343D GLY* 1.3 63.4 + - - +
345D LYS* 3.4 4.6 + - - +
346D ALA* 3.0 22.0 + - - +
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Residues in contact with GLY 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D PHE* 4.6 5.8 - - - -
308D ILE* 4.2 4.0 - - - +
325D VAL* 3.4 6.7 - - - +
326D LYS 3.7 19.1 - - - -
327D THR* 4.6 0.4 - - - -
328D PRO* 4.2 7.9 - - - +
339D ALA 3.0 11.0 + - - -
340D ASN 3.0 6.7 + - - -
342D ALA* 1.3 77.3 - - - +
344D ILE* 1.3 55.1 + - - +
346D ALA* 3.4 1.7 + - - +
347D THR* 2.6 33.6 + - - -
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Residues in contact with ILE 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ALA* 4.7 7.9 - - + -
65D PRO* 3.8 34.5 - - + -
82D LEU* 4.0 27.4 - - + +
86D GLY* 3.2 22.4 - - - +
87D GLY 4.2 1.6 - - - -
88D ALA* 3.9 17.3 - - + +
325D VAL* 3.9 18.2 - - + -
340D ASN* 3.0 22.2 + - - +
341D ALA* 3.8 4.9 - - - +
343D GLY* 1.3 76.3 - - - +
345D LYS* 1.3 56.4 + - - +
347D THR* 3.3 3.4 + - - -
348D LYS* 2.8 37.0 + - + +
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Residues in contact with LYS 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ASP* 2.7 34.4 + - - +
302B SER* 4.0 10.1 + - - -
303B LYS* 4.1 26.6 - - + +
85D GLU* 3.7 26.4 + - - +
86D GLY 3.8 15.5 - - - +
341D ALA* 2.9 32.7 + - - +
342D ALA* 3.8 9.8 - - - +
344D ILE* 1.3 76.2 - - - +
346D ALA* 1.3 56.6 + - - +
348D LYS* 3.5 3.3 + - - +
349D MET* 2.9 30.8 + - - +
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Residues in contact with ALA 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B SER 3.5 24.6 + - - +
306B GLY* 3.9 5.2 - - - +
305D PHE* 3.7 23.1 - - + -
308D ILE* 4.6 2.0 - - + -
309D VAL* 4.0 16.4 - - + +
342D ALA 3.0 17.6 + - - +
343D GLY 3.9 3.6 - - - +
345D LYS* 1.3 75.8 - - - +
347D THR* 1.3 57.9 + - - +
349D MET* 3.5 3.8 + - - +
350D ALA* 3.0 29.1 + - - +
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Residues in contact with THR 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ALA* 4.3 6.5 - - + -
292D GLN* 3.6 20.2 + - - +
308D ILE* 3.7 6.7 - - - +
309D VAL* 5.5 0.2 - - - -
312D THR* 3.4 31.6 - - + +
323D VAL* 4.0 19.3 - - + -
325D VAL* 3.8 15.9 - - + +
343D GLY 2.6 24.3 + - - -
344D ILE 3.4 4.3 - - - -
346D ALA* 1.3 73.8 - - - +
348D LYS* 1.3 61.4 + - - +
350D ALA* 3.1 2.6 + - - -
351D LEU* 2.9 28.1 + - + +
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Residues in contact with LYS 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D THR 5.2 3.8 + - - -
63D ALA* 3.8 18.6 - - + -
86D GLY 4.5 1.1 - - - +
87D GLY* 2.9 36.1 - - - +
89D ASP* 2.9 32.0 + - - +
344D ILE* 2.8 27.4 + - + +
345D LYS* 4.2 3.8 - - - +
347D THR* 1.3 70.4 - - - +
349D MET* 1.3 62.0 + - - +
351D LEU* 3.2 10.6 + - + +
352D ASN* 2.9 51.3 + - - +
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Residues in contact with MET 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B PRO* 4.3 2.7 - - + -
303B LYS* 3.2 47.1 - - + +
306B GLY* 4.3 3.8 - - - -
307B VAL* 3.8 17.5 - - + -
473B VAL* 3.4 24.7 - - + +
476B GLY* 3.6 35.0 - - - +
477B ARG 3.9 0.2 - - - +
345D LYS 2.9 19.5 + - - +
346D ALA 3.7 4.5 - - - +
348D LYS* 1.3 75.2 - - - +
350D ALA* 1.3 57.7 + - - +
352D ASN* 3.2 2.3 + - - +
353D MET* 2.8 61.1 + - + +
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Residues in contact with ALA 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B GLY* 4.4 2.9 - - - +
310B THR* 3.6 28.3 - - + -
309D VAL* 3.9 12.8 - - + -
312D THR* 3.7 17.3 - - + -
313D THR* 4.9 0.9 - - - +
346D ALA 3.0 13.6 + - - +
347D THR 3.5 8.5 - - - +
349D MET* 1.3 77.1 - - - +
351D LEU* 1.3 62.5 + - - +
353D MET* 3.2 12.1 + - - +
354D LEU* 3.2 24.2 + - + +
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Residues in contact with LEU 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D THR* 3.4 54.3 - - + +
63D ALA* 4.4 9.0 - - + -
312D THR* 3.6 20.0 - - + +
315D ALA* 5.3 0.2 - - + -
316D ALA* 3.9 18.9 - - + +
323D VAL* 4.1 14.4 - - + -
347D THR* 2.9 23.4 + - + +
348D LYS* 3.2 16.6 + - + +
350D ALA* 1.3 73.7 - - - +
352D ASN* 1.3 64.3 + - - +
354D LEU* 3.1 20.4 + - - +
355D GLU* 3.2 12.5 + - - -
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Residues in contact with ASN 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B GLY 3.3 27.0 + - - +
477B ARG* 3.7 27.4 + - + +
478B LEU* 3.2 17.4 + - - +
348D LYS* 2.9 38.9 + - - +
349D MET* 3.8 1.3 - - - +
351D LEU* 1.3 81.0 - - - +
353D MET* 1.3 59.3 + - - +
354D LEU 3.1 1.2 + - - -
355D GLU* 3.6 18.2 + - - +
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Residues in contact with MET 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B GLU* 4.7 12.3 - - - +
256B GLY* 3.9 3.7 - - - +
293B TRP* 5.1 5.4 - - + -
307B VAL* 4.3 19.7 - - + -
310B THR* 4.4 15.3 - - - +
473B VAL* 3.8 29.4 - - + -
477B ARG 4.0 0.2 - - - -
478B LEU* 3.5 55.7 - - + +
349D MET* 2.8 51.5 + - + +
350D ALA* 3.2 9.8 + - - +
352D ASN* 1.3 76.0 - - - +
354D LEU* 1.3 64.5 + - + +
355D GLU 3.6 0.4 - - - -
357D GLN* 3.6 3.8 + - - -
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Residues in contact with LEU 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B GLY 4.5 5.6 - - - +
258B MET* 5.2 9.2 - - + -
310B THR* 4.4 13.5 - - + -
314B ILE* 5.4 4.5 - - + -
313D THR* 3.8 45.1 - - + +
316D ALA* 3.8 20.9 - - + +
317D LEU* 5.1 7.6 - - + -
350D ALA 3.4 19.3 - - - +
351D LEU 3.1 7.8 + - - +
353D MET* 1.3 86.5 - - + +
355D GLU* 1.3 65.7 + - - +
356D GLY 3.1 0.7 + - - -
357D GLN* 2.9 47.6 + - + +
358D ARG* 5.0 0.9 + - - -
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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