Contacts of the helix formed by residues 305 - 320 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A PHE* 4.1 21.1 - - - -
246A ASP* 6.1 1.1 - - - -
250A MET* 5.1 2.7 - - - -
301A PRO* 2.7 17.7 + - - +
302A GLN 3.5 4.9 - - - +
304A PHE* 1.3 72.4 - - - +
306A THR* 1.3 61.0 + - - +
307A THR* 2.9 23.9 + - - -
308A VAL* 3.3 17.2 + - - +
309A TRP 3.3 14.7 + - - -
575A ARG* 3.4 7.1 + - - -
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Residues in contact with THR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE 3.8 2.6 + - - +
305A SER* 1.3 71.4 + - - +
307A THR* 1.3 72.8 + - - +
309A TRP* 3.6 17.4 - - + +
310A GLN* 3.1 23.2 + - - +
575A ARG* 3.5 28.3 - - - +
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Residues in contact with THR 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 6.1 0.7 - - - -
189A LEU* 6.0 8.9 - - + +
240A GLY 3.8 15.9 + - - +
241A LEU* 2.8 33.8 + - - +
246A ASP* 5.5 0.2 + - - -
305A SER* 2.9 8.1 + - - -
306A THR* 1.3 81.5 - - - +
308A VAL* 1.3 67.9 + - - +
310A GLN* 3.3 12.7 + - - +
311A PHE* 3.0 21.7 + - - +
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 4.0 17.7 - - + +
242A PHE* 4.0 20.2 - - + -
301A PRO* 4.1 5.2 - - + -
302A GLN* 3.9 12.6 - - - +
305A SER* 3.3 21.7 + - - +
307A THR* 1.3 80.9 + - - +
309A TRP* 1.3 66.1 + - - +
311A PHE* 3.0 6.4 + - + +
312A LEU* 2.9 34.9 + - + +
325A SER* 3.9 22.0 - - - +
418A LEU* 4.1 22.7 - - + -
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Residues in contact with TRP 309 (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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302A GLN* 3.6 21.3 - - - +
305A SER 3.3 16.2 + - - +
306A THR* 3.6 20.9 - - + +
307A THR 3.2 0.4 - - - -
308A VAL* 1.3 80.0 - - - +
310A GLN* 1.3 51.7 + - - +
312A LEU* 3.2 2.1 + - - +
313A ALA* 2.6 39.8 + - + +
510A LEU* 4.1 14.4 - - + -
511A PRO* 2.9 49.5 + - + +
512A PRO 3.8 13.9 - - - -
513A VAL* 3.8 18.4 - - + -
575A ARG* 3.7 42.6 - - + -
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Residues in contact with GLN 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 3.8 38.5 + - + +
192A LEU* 5.9 3.4 - - + +
306A THR 3.1 14.7 + - - +
307A THR* 3.3 9.4 + - - +
309A TRP* 1.3 79.9 - - - +
311A PHE* 1.3 63.2 + - - +
313A ALA* 3.8 0.3 - - - +
314A VAL* 3.0 36.1 + - + +
513A VAL* 3.5 38.5 - - + +
514A LEU 5.7 2.6 + - - -
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Residues in contact with PHE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 4.3 11.2 - - + -
189A LEU* 5.3 5.6 - - + +
205A LEU* 3.8 36.9 - - + +
208A TRP* 4.0 18.2 - + - -
209A LEU* 3.9 24.0 - - + -
241A LEU* 4.1 20.0 - - + -
307A THR 3.0 12.4 + - - +
308A VAL* 3.0 15.0 + - + +
310A GLN* 1.3 78.8 - - - +
312A LEU* 1.3 65.9 + - + +
314A VAL* 3.4 2.4 + - - +
315A LEU* 3.1 53.2 + - + +
349A LEU* 3.9 22.4 - - + -
418A LEU* 5.5 5.8 - - + -
420A LEU* 4.5 4.9 - - + -
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A GLN* 3.4 46.4 - - + +
308A VAL* 2.9 19.3 + - + +
311A PHE* 1.3 82.8 - - + +
313A ALA* 1.3 67.5 + - - +
315A LEU* 4.4 2.7 - - + +
316A GLN* 3.0 27.5 + - - +
323A ALA* 3.5 20.8 - - + +
324A GLY 3.6 6.5 - - - +
325A SER* 3.7 15.3 - - - +
418A LEU* 5.9 1.3 - - + -
420A LEU* 3.4 33.4 - - + -
510A LEU* 3.6 13.9 - - + -
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Residues in contact with ALA 313 (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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309A TRP* 2.6 29.5 + - + +
310A GLN 3.8 3.8 - - - +
312A LEU* 1.3 73.7 - - - +
314A VAL* 1.3 60.2 + - - +
316A GLN* 3.0 34.0 + - - +
317A GLU* 4.2 4.3 + - - +
510A LEU* 3.9 5.5 - - + +
511A PRO 3.7 23.6 - - - +
512A PRO* 4.9 1.5 - - + +
513A VAL* 4.1 16.6 - - + +
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Residues in contact with VAL 314 (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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192A LEU* 4.3 15.9 - - + -
198A SER 5.4 0.4 - - - +
201A ARG* 3.7 15.3 - - + +
202A ALA* 3.3 41.1 - - - +
205A LEU* 3.7 23.8 - - + -
310A GLN* 3.0 22.6 + - + +
313A ALA* 1.3 78.7 - - - +
315A LEU* 1.3 62.9 + - - +
317A GLU* 3.4 11.9 + - - +
513A VAL* 3.9 20.0 - - + -
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ALA 4.4 2.0 - - - +
205A LEU* 4.0 15.5 - - + +
206A PHE* 3.8 42.6 - - + +
209A LEU* 4.2 4.3 - - + -
311A PHE* 3.1 44.1 + - + +
312A LEU* 3.4 4.9 + - - +
314A VAL* 1.3 73.0 - - - +
316A GLN* 1.3 64.9 + - - +
318A GLN* 3.0 29.7 + - - +
319A PHE* 3.0 20.4 + - + -
323A ALA* 4.8 2.5 - - + -
420A LEU* 3.7 30.7 - - + -
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Residues in contact with GLN 316 (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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312A LEU 3.0 12.8 + - - +
313A ALA* 3.0 32.3 + - - +
315A LEU* 1.3 75.6 - - - +
317A GLU* 1.3 64.5 + - + +
319A PHE* 3.0 0.8 + - - -
320A GLY 3.0 20.8 + - - -
321A SER 3.6 22.2 + - - +
322A MET* 5.3 2.6 - - - +
323A ALA* 4.2 16.9 + - - +
505A PHE* 3.8 12.8 - - + -
509A SER* 3.5 22.2 + - - -
510A LEU* 3.1 48.9 + - - +
511A PRO 5.5 0.4 - - - -
512A PRO* 5.7 1.2 - - - +
554A GLY 5.3 4.4 + - - -
570A THR* 5.8 0.4 + - - +
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Residues in contact with GLU 317 (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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198A SER* 3.1 41.9 + - - +
199A ARG* 3.2 23.2 + - + +
202A ALA* 3.8 4.9 - - + -
313A ALA 4.7 4.9 - - - +
314A VAL* 3.4 14.8 + - - +
315A LEU 3.1 0.2 - - - -
316A GLN* 1.3 86.4 - - + +
318A GLN* 1.3 60.1 + - - +
319A PHE 3.4 0.2 + - - -
320A GLY* 3.6 8.7 + - - -
505A PHE* 4.9 6.6 - - + -
552A GLN* 4.0 8.5 - - - +
553A ASP* 4.1 8.0 - - - +
554A GLY* 4.1 24.2 + - - -
456B ARG 5.3 0.5 - - - +
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Residues in contact with GLN 318 (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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199A ARG 5.4 0.7 - - - +
202A ALA* 3.5 36.7 - - + +
203A ALA* 4.3 5.6 - - + +
206A PHE* 3.3 25.8 - - + +
219A TYR* 2.7 24.1 + - - -
315A LEU* 3.0 24.5 + - - +
317A GLU* 1.3 79.1 - - - +
319A PHE* 1.3 94.2 + - - +
320A GLY 3.5 0.2 - - - -
456B ARG* 3.1 30.8 + - - +
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Residues in contact with PHE 319 (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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206A PHE* 4.0 9.6 - + - -
219A TYR* 3.4 21.5 - - - -
223A TRP* 4.1 14.1 - + - -
315A LEU* 3.0 34.4 + - + +
316A GLN 3.0 2.0 + - - +
318A GLN* 1.3 92.8 - - - +
320A GLY* 1.3 62.4 + - - +
321A SER 2.9 18.7 + - - +
323A ALA* 4.3 7.0 - - + -
347A PHE* 3.5 33.0 - + - -
420A LEU* 4.6 17.7 - - + -
422A THR* 4.0 32.1 - - + +
423A TYR* 3.3 20.5 - + + -
456B ARG* 3.6 16.7 - - - +
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Residues in contact with GLY 320 (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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316A GLN 3.0 8.2 + - - -
317A GLU 3.6 6.7 + - - -
318A GLN 3.5 2.4 - - - -
319A PHE* 1.3 77.6 - - - +
321A SER* 1.3 59.0 + - - +
423A TYR* 5.1 0.4 - - - -
426A ASN* 4.5 7.8 + - - +
505A PHE* 4.0 10.5 - - - +
456B ARG* 3.2 20.5 + - - +
458B PHE* 5.7 1.6 - - - -
459B MET* 3.3 28.6 - - - +
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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
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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