Contacts of the helix formed by residues 305 - 320 (chain B) in PDB entry 4CCN
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 SER 305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LEU 4.0 2.1 + - - -
242B PHE* 4.1 18.8 - - - -
246B ASP* 6.0 0.9 - - - -
250B MET* 5.7 0.4 - - - +
301B PRO 2.8 17.7 + - - -
302B GLN 3.6 2.1 - - - +
304B PHE* 1.3 72.5 - - - +
306B THR* 1.3 61.7 + - - +
307B THR* 2.9 24.4 + - - +
308B VAL* 3.1 21.1 + - - +
309B TRP* 3.1 17.5 + - - +
575B ARG* 3.2 6.6 + - - -
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Residues in contact with THR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B PHE 3.4 3.6 + - - +
305B SER* 1.3 72.9 + - - +
307B THR* 1.3 66.2 + - - +
309B TRP* 3.4 17.8 + - + +
310B GLN* 3.0 29.5 + - - +
575B ARG* 3.5 27.1 - - - +
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Residues in contact with THR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 6.1 0.4 - - - -
189B LEU* 5.7 11.7 - - + +
240B GLY 3.5 19.7 + - - +
241B LEU* 2.9 30.2 + - - +
305B SER* 2.9 10.8 + - - +
306B THR* 1.3 81.7 - - - +
308B VAL* 1.3 61.3 + - - +
310B GLN* 3.6 10.7 + - - +
311B PHE* 3.1 23.6 + - - +
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 3.6 21.1 - - + +
242B PHE* 4.0 11.0 - - + -
301B PRO* 3.9 12.6 - - + -
302B GLN* 3.9 12.3 - - + +
305B SER* 3.1 27.4 + - - +
307B THR* 1.3 79.3 + - - +
309B TRP* 1.3 67.5 + - - +
311B PHE* 3.2 7.9 + - + +
312B LEU* 2.9 29.0 + - + +
325B SER* 3.9 21.3 - - - +
418B LEU* 4.1 20.2 - - + -
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Residues in contact with TRP 309 (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 GLN* 3.6 22.6 - - + +
305B SER 3.1 16.2 + - - +
306B THR* 3.5 20.4 - - + +
308B VAL* 1.3 79.1 - - - +
310B GLN* 1.3 51.6 + - - +
312B LEU* 3.7 1.4 - - - +
313B ALA* 2.6 45.9 + - + +
510B LEU* 4.1 14.6 - - + -
511B PRO* 2.7 50.0 + - + +
512B PRO 3.7 8.7 - - - -
513B VAL* 3.7 22.4 - - + -
575B ARG* 3.7 40.4 - - + +
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Residues in contact with GLN 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 4.0 40.0 + - + +
192B LEU* 5.0 8.9 - - - +
193B ASN* 5.4 5.1 + - - -
205B LEU* 6.3 0.2 - - + -
306B THR 3.0 17.8 + - - +
307B THR* 3.9 9.8 - - - +
309B TRP* 1.3 76.8 - - - +
311B PHE* 1.3 65.1 + - - +
313B ALA* 3.8 0.6 - - - +
314B VAL* 3.0 34.7 + - + +
513B VAL* 3.8 37.5 - - + +
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Residues in contact with PHE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 3.8 17.7 - - + -
189B LEU* 5.0 5.8 - - + -
205B LEU* 3.6 34.3 - - + +
208B TRP* 3.8 27.4 - + - -
209B LEU* 4.1 16.2 - - + -
241B LEU* 4.1 19.1 - - + -
307B THR 3.1 17.7 + - - +
308B VAL* 3.4 7.4 - - + +
310B GLN* 1.3 80.6 - - - +
312B LEU* 1.3 70.5 + - + +
314B VAL 3.4 0.2 + - - -
315B LEU* 3.1 52.2 + - + +
349B LEU* 4.4 20.0 - - + -
418B LEU* 5.8 5.2 - - + -
420B LEU* 4.7 3.4 - - + -
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLN* 3.7 28.5 - - + +
308B VAL* 2.9 21.7 + - + +
309B TRP* 3.8 1.8 - - - +
311B PHE* 1.3 82.5 - - + +
313B ALA* 1.3 66.0 + - - +
314B VAL 3.0 2.4 + - - -
315B LEU* 4.4 2.7 - - + +
316B GLN* 3.0 28.2 + - - +
323B ALA* 3.2 26.4 - - + +
324B GLY 3.7 6.5 - - - +
325B SER* 3.6 25.8 - - - +
418B LEU* 5.7 2.0 - - + -
420B LEU* 3.2 36.1 - - + -
510B LEU* 3.9 7.6 - - + -
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Residues in contact with ALA 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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309B TRP* 2.6 44.1 + - + +
310B GLN* 3.8 6.7 - - - +
312B LEU* 1.3 73.9 - - - +
314B VAL* 1.3 58.5 + - - +
316B GLN* 2.9 32.8 + - - +
317B GLU* 4.4 2.9 + - - +
510B LEU* 4.1 7.5 - - + +
511B PRO 3.8 11.2 - - - +
512B PRO* 5.0 2.3 - - + +
513B VAL* 4.5 11.0 - - + +
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Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LEU* 4.5 14.1 - - + -
198B SER 5.3 0.7 - - - +
201B ARG* 4.0 13.7 - - + +
202B ALA* 3.2 44.5 - - + +
205B LEU* 3.8 17.7 - - + -
310B GLN* 3.0 24.7 + - + +
311B PHE 3.7 3.4 - - - +
313B ALA* 1.3 77.9 - - - +
315B LEU* 1.3 65.4 + - - +
316B GLN 3.3 0.2 - - - -
317B GLU* 3.3 11.7 + - - +
513B VAL* 4.0 18.4 - - + -
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Residues in contact with LEU 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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202B ALA 4.5 1.6 - - - +
205B LEU* 3.7 27.1 - - + +
206B PHE* 3.8 31.2 - - + +
209B LEU* 4.2 6.1 - - + -
311B PHE* 3.1 41.7 + - + +
312B LEU* 4.0 4.7 - - + +
314B VAL* 1.3 79.0 - - - +
316B GLN* 1.3 64.3 + - - +
318B GLN* 3.2 13.4 + - - +
319B PHE* 3.1 34.1 + - + -
323B ALA* 4.7 2.5 - - + -
420B LEU* 3.5 34.8 - - + -
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Residues in contact with GLN 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU 3.0 12.9 + - - +
313B ALA* 2.9 30.1 + - - +
315B LEU* 1.3 76.0 - - - +
317B GLU* 1.3 56.0 + - - +
319B PHE* 3.0 2.4 + - - -
320B GLY* 2.8 32.6 + - - -
321B SER 3.6 20.9 + - - +
322B MET* 5.2 1.9 - - - +
323B ALA* 4.1 16.3 + - - +
505B PHE* 3.9 12.1 - - + -
509B SER* 3.5 21.5 + - - -
510B LEU* 3.0 45.7 + - - +
512B PRO* 6.1 0.8 - - - +
554B GLY 5.4 4.9 + - - -
570B THR* 5.9 0.2 + - - -
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Residues in contact with GLU 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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456A ARG 5.2 1.2 - - - +
198B SER* 2.8 45.7 + - - +
199B ARG* 4.1 7.9 - - + -
202B ALA* 3.8 7.7 - - + +
313B ALA 4.8 4.0 - - - +
314B VAL* 3.3 14.8 + - - +
315B LEU 3.1 0.6 - - - -
316B GLN* 1.3 84.9 - - + +
318B GLN* 1.3 61.4 + - - +
320B GLY* 3.6 7.6 + - - -
505B PHE* 5.0 6.2 - - - -
552B GLN* 4.8 3.5 - - - +
553B ASP* 3.6 10.3 - - - +
554B GLY* 3.2 33.2 + - - -
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Residues in contact with GLN 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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456A ARG* 3.0 35.3 + - - +
199B ARG 5.5 0.4 - - - +
202B ALA* 3.5 37.8 - - + +
203B ALA* 4.4 6.0 - - + +
206B PHE* 3.4 25.8 - - + +
219B TYR* 2.7 24.1 + - - -
315B LEU* 3.2 13.3 + - - +
317B GLU* 1.3 77.3 - - - +
319B PHE* 1.3 107.1 + - - +
320B GLY 3.4 0.4 - - - -
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Residues in contact with PHE 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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456A ARG* 3.7 11.6 - - - +
206B PHE* 4.0 8.1 - + - -
219B TYR* 3.4 16.2 - - - -
223B TRP* 3.9 21.5 - + - -
315B LEU* 3.1 32.4 + - + -
316B GLN 3.0 3.6 + - - +
318B GLN* 1.3 98.9 - - - +
320B GLY* 1.3 62.4 + - - +
321B SER 2.9 18.3 + - - +
323B ALA* 4.3 6.3 - - + -
347B PHE* 3.6 25.8 - + - -
420B LEU* 4.5 16.4 - - + -
422B THR* 3.8 35.9 - - + +
423B TYR* 3.3 23.8 + - + -
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Residues in contact with GLY 320 (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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456A ARG* 3.5 16.6 + - - -
458A PHE* 5.7 2.6 - - - -
459A MET* 3.4 27.9 - - - +
316B GLN 2.8 9.5 + - - -
317B GLU 3.6 6.3 + - - -
318B GLN 3.4 2.6 - - - -
319B PHE* 1.3 78.4 - - - +
321B SER* 1.3 57.9 + - - +
423B TYR* 5.2 0.2 - - - -
426B ASN* 4.8 7.0 + - - +
505B PHE* 3.8 14.8 - - - +
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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