Contacts of the helix formed by residues 300 - 319 (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 ASP 300 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B PRO* 3.4 2.2 - - - +
299B GLN* 1.3 80.4 - - - +
301B GLU* 1.3 60.4 + - - +
302B SER* 2.9 31.3 + - - -
303B LYS* 3.0 38.4 + - + +
304B ALA* 3.0 26.2 + - - +
345D LYS* 2.7 32.0 + - - +
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Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LYS* 3.7 15.6 + - - -
299B GLN 3.2 5.1 + - - +
300B ASP* 1.3 75.0 + - - +
302B SER* 1.3 63.0 + - - +
304B ALA* 3.2 9.8 + - - +
305B PHE* 3.0 34.1 + - + -
328B PRO* 3.7 31.1 - - + +
329B HIS* 3.6 24.7 + - - -
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Residues in contact with SER 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ASP* 2.9 10.7 + - - -
301B GLU* 1.3 75.5 - - - +
303B LYS* 1.3 66.5 + - - +
305B PHE* 3.1 19.1 + - - +
306B GLY 3.1 8.8 + - - -
305D PHE* 3.9 8.4 - - - -
342D ALA* 3.2 46.2 - - - +
345D LYS* 4.0 12.2 + - - -
346D ALA* 3.5 12.5 - - - +
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PRO* 3.7 22.7 - - + -
300B ASP* 3.0 31.2 + - + +
302B SER* 1.3 76.3 - - - +
304B ALA* 1.3 61.5 + - - +
306B GLY 2.9 11.1 + - - -
307B VAL* 3.1 10.7 + - - +
475B LYS 5.4 3.2 + - - -
476B GLY* 5.0 9.4 - - - -
345D LYS* 4.1 39.0 - - + +
349D MET* 3.2 33.1 - - + +
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B PHE* 3.6 28.4 - - + -
298B PRO* 3.7 9.1 - - - +
300B ASP 3.0 13.5 + - - +
301B GLU* 3.4 10.1 - - - +
302B SER 3.2 0.2 - - - -
303B LYS* 1.3 76.1 - - - +
305B PHE* 1.3 56.1 + - - +
307B VAL* 3.0 5.1 + - - +
308B ILE* 2.9 32.0 + - - +
328B PRO* 3.7 27.1 - - + +
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Residues in contact with PHE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B GLU* 3.0 33.6 + - + -
302B SER 3.1 7.2 + - - +
304B ALA* 1.3 75.1 - - - +
306B GLY* 1.3 63.4 + - - +
308B ILE* 4.2 9.9 - - + -
309B VAL* 2.9 30.2 + - + +
328B PRO* 3.7 28.3 - - + -
342B ALA* 3.9 15.9 - - + -
343B GLY* 4.6 2.0 - - - -
346B ALA* 3.7 31.6 - - + -
302D SER* 3.9 20.0 - - - -
305D PHE* 3.6 50.9 - + + -
309D VAL* 4.1 2.9 - - + +
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Residues in contact with GLY 306 (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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302B SER 3.1 7.9 + - - -
303B LYS 2.9 9.3 + - - -
305B PHE* 1.3 76.8 - - - +
307B VAL* 1.3 50.4 + - - +
310B THR* 2.7 42.4 + - - +
309D VAL* 3.6 10.8 - - - +
346D ALA 3.9 20.4 - - - -
349D MET* 4.3 8.3 - - - -
350D ALA* 4.5 2.1 - - - -
353D MET* 5.4 0.7 - - - -
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Residues in contact with VAL 307 (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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254B GLU* 4.8 1.3 - - - +
292B GLN* 6.0 0.2 - - + -
293B TRP* 3.6 34.8 - - + +
297B PHE* 3.6 18.4 - - + -
298B PRO* 4.1 10.1 - - + -
303B LYS 3.1 7.4 + - - +
304B ALA 3.0 7.1 + - - +
306B GLY* 1.3 73.3 - - - +
308B ILE* 1.3 67.6 + - - +
310B THR* 3.2 5.2 + - - +
311B ALA* 2.9 27.5 + - - +
473B VAL* 4.0 12.3 - - + -
349D MET* 3.8 30.1 - - + -
353D MET* 4.3 12.6 - - + -
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Residues in contact with ILE 308 (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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292B GLN* 3.6 21.2 + - - +
297B PHE* 4.0 10.5 - - + -
304B ALA 2.9 24.9 + - - +
305B PHE* 3.8 13.9 - - + +
307B VAL* 1.3 76.8 - - - +
309B VAL* 1.3 68.6 + - + +
311B ALA* 3.5 3.4 + - - +
312B THR* 2.9 30.0 + - - +
326B LYS 3.3 26.7 - - - +
327B THR* 3.7 22.9 - - - -
328B PRO* 3.9 9.0 - - + -
343B GLY* 4.2 7.4 - - - +
346B ALA* 4.6 4.7 - - + -
347B THR* 3.7 20.0 - - - +
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B PHE* 2.9 21.3 + - + +
308B ILE* 1.3 78.9 - - + +
310B THR* 1.3 67.4 + - - +
312B THR* 3.3 5.1 + - - -
313B THR* 3.0 26.5 + - - -
346B ALA* 4.0 31.6 - - + +
350B ALA* 3.9 6.5 - - + +
305D PHE 4.1 5.2 - - - +
306D GLY* 3.6 29.4 - - - +
309D VAL* 3.5 24.2 - - + -
310D THR* 3.6 15.0 - - + +
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Residues in contact with THR 310 (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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254B GLU* 5.0 3.2 + - - -
306B GLY 2.7 25.3 + - - +
307B VAL* 3.2 8.7 + - - -
309B VAL* 1.3 76.9 - - - +
311B ALA* 1.3 64.0 + - - +
313B THR* 3.1 13.1 + - - -
314B ILE* 3.1 20.8 + - - +
309D VAL* 3.7 2.7 - - + -
313D THR* 3.4 27.0 - - - +
350D ALA* 3.6 27.4 - - + +
353D MET* 4.4 13.8 - - + +
354D LEU* 4.4 17.0 - - + -
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B GLU* 3.1 35.6 + - - +
290B PHE* 3.5 8.7 - - + -
292B GLN* 3.7 26.2 - - + -
293B TRP 4.3 0.2 - - - +
307B VAL 2.9 18.2 + - - +
308B ILE 3.6 4.9 - - - +
310B THR* 1.3 78.6 + - - +
312B THR* 1.3 61.3 + - - +
314B ILE* 3.2 7.3 + - - +
315B ALA* 3.0 18.2 + - - +
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Residues in contact with THR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLN* 3.0 19.6 + - - +
308B ILE 2.9 22.0 + - - -
309B VAL* 3.6 5.8 - - - -
310B THR 3.2 0.2 - - - -
311B ALA* 1.3 75.9 - - - +
313B THR* 1.3 57.2 + - - +
315B ALA* 3.2 6.5 + - - +
316B ALA* 2.9 28.5 + - - +
323B VAL* 4.9 3.4 - - + -
347B THR* 3.4 37.6 + - + +
350B ALA* 3.8 14.1 - - + -
351B LEU* 3.5 21.5 - - + +
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Residues in contact with THR 313 (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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258B MET* 4.2 2.0 - - + -
309B VAL 3.0 14.7 + - - -
310B THR 3.1 10.5 + - - -
312B THR* 1.3 76.0 - - - +
314B ILE* 1.3 63.1 + - - +
316B ALA* 3.4 1.2 + - - +
317B LEU* 3.0 34.2 + - + +
350B ALA* 5.2 0.4 - - - +
354B LEU* 3.8 22.2 - - + +
258D MET* 3.9 16.8 - - + -
310D THR* 3.4 27.3 - - + +
313D THR* 3.7 30.3 + - + -
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Residues in contact with ILE 314 (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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254B GLU* 3.5 26.7 - - - +
256B GLY 4.0 14.1 - - - +
258B MET* 3.8 33.7 - - + +
261B ASP* 3.6 29.2 - - + +
262B ILE* 4.1 12.5 - - + +
290B PHE* 3.5 20.9 - - + -
310B THR* 3.1 16.8 + - - +
311B ALA* 3.2 5.6 + - - +
313B THR* 1.3 77.3 - - - +
315B ALA* 1.3 62.0 + - - +
317B LEU* 3.8 2.3 - - - +
318B ALA* 3.0 23.4 + - + +
354D LEU* 5.4 5.8 - - + -
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Residues in contact with ALA 315 (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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61B THR* 4.3 3.8 + - + -
290B PHE* 3.6 37.9 - - + -
311B ALA 3.0 8.9 + - - +
312B THR* 3.4 8.7 - - + +
314B ILE* 1.3 78.4 - - - +
316B ALA* 1.3 62.2 + - - +
318B ALA* 3.3 5.0 + - - +
319B GLY 3.2 3.8 + - - -
320B ALA* 3.1 29.2 + - + -
323B VAL* 4.0 21.3 - - + -
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Residues in contact with ALA 316 (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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61B THR* 4.2 11.4 + - - -
312B THR 2.9 17.1 + - - +
313B THR 3.6 4.7 - - - +
315B ALA* 1.3 76.7 - - - +
317B LEU* 1.3 57.5 + - + +
319B GLY* 3.0 19.2 + - - -
351B LEU* 3.9 17.6 - - + +
354B LEU* 3.9 30.1 - - + +
357B GLN 3.5 12.9 - - - +
358B ARG* 3.8 6.7 + - - +
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Residues in contact with LEU 317 (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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258B MET* 3.9 21.1 - - + -
262B ILE* 4.1 10.8 - - + -
266B ARG* 2.9 20.8 + - - -
313B THR* 3.0 23.7 + - + +
314B ILE 4.0 2.5 - - - +
316B ALA* 1.3 77.2 - - + +
318B ALA* 1.3 56.8 + - - +
319B GLY 3.3 0.6 + - - -
354B LEU* 5.1 5.8 - - + -
357B GLN* 3.7 40.2 - - + +
358B ARG* 3.5 11.6 - - - +
359B MET* 2.9 22.5 + - + +
258D MET* 3.6 40.2 - - + -
359D MET* 5.4 0.2 - - + -
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Residues in contact with ALA 318 (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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261B ASP 5.2 0.2 - - - +
262B ILE* 3.8 27.7 - - + +
265B LEU* 3.9 25.7 - - + +
266B ARG* 3.8 25.2 + - - +
290B PHE* 5.3 1.3 - - + -
314B ILE* 3.0 20.3 + - + +
315B ALA* 3.5 7.9 - - - +
317B LEU* 1.3 77.7 - - - +
319B GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 319 (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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56B LYS* 4.7 9.5 + - - -
61B THR* 4.9 1.1 - - - -
265B LEU* 4.9 0.4 - - - -
269B GLU* 5.3 1.9 - - - +
288B THR* 4.0 3.9 + - - -
316B ALA 3.0 11.9 + - - -
317B LEU 3.3 1.4 + - - -
318B ALA* 1.3 79.6 - - - +
320B ALA* 1.3 66.8 + - - +
321B THR* 3.4 3.1 + - - -
358B ARG* 3.5 30.1 + - - -
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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