Contacts of the helix formed by residues 314 - 330 (chain B) in PDB entry 1C1D
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 ALA 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B GLU 3.0 13.2 + - - +
311B ARG* 3.1 19.9 + - - +
313B VAL* 1.3 72.3 - - - +
315B ILE* 1.3 64.0 + - - +
316B GLY 3.0 2.5 - - - -
317B ASP* 3.0 14.2 + - + +
318B THR* 3.0 24.0 + - - +
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Residues in contact with ILE 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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70B SER* 5.7 0.9 - - - +
156B GLY* 3.8 28.9 - - - +
159B GLU* 5.4 0.2 - - + -
160B ALA* 4.0 14.8 - - + -
286B VAL* 3.6 31.4 - - + +
287B ALA* 4.0 5.2 - - - +
289B ALA* 4.1 2.2 - - + -
290B GLY* 3.6 28.5 - - - +
293B ILE* 3.9 21.8 - - + -
311B ARG 3.6 1.5 + - - +
312B ALA* 3.0 19.5 + - - +
313B VAL 3.0 0.6 + - - -
314B ALA* 1.3 77.4 - - - +
316B GLY* 1.3 60.5 + - - +
318B THR* 3.2 10.9 + - - +
319B LEU* 2.9 22.6 + - + +
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Residues in contact with GLY 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLU* 4.1 14.7 - - - +
160B ALA* 4.8 0.4 - - - -
163B ALA* 3.7 23.2 - - - +
313B VAL 3.1 10.6 + - - -
314B ALA 3.0 1.4 - - - -
315B ILE* 1.3 79.0 - - - +
317B ASP* 1.3 56.5 + - - +
319B LEU* 3.3 2.4 + - - -
320B ASN* 2.9 33.6 + - - -
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Residues in contact with ASP 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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313B VAL 4.5 0.6 + - - -
314B ALA* 3.0 18.7 + - + +
316B GLY* 1.3 73.7 - - - +
318B THR* 1.3 66.4 + - - +
320B ASN* 3.1 15.3 + - - +
321B GLN* 2.8 50.4 + - - +
344B ARG* 4.6 1.6 + - - -
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 4.1 14.7 + - + +
70B SER* 5.8 0.7 - - - -
286B VAL* 3.7 19.5 - - + -
314B ALA* 3.0 13.5 + - - +
315B ILE* 3.2 14.6 + - - +
317B ASP* 1.3 77.7 + - - +
319B LEU* 1.3 62.5 + - - +
321B GLN* 3.0 6.9 + - - +
322B VAL* 3.0 20.5 + - + +
340B LEU* 3.9 13.5 - - + -
344B ARG* 3.2 37.9 + - - +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ALA* 3.2 48.2 - - + +
163B ALA* 4.6 2.9 - - + -
164B THR* 4.2 1.1 - - - +
282B ALA* 4.0 11.0 - - + -
283B PRO* 3.7 29.8 - - + +
286B VAL* 3.6 23.1 - - + -
287B ALA* 4.7 1.6 - - + -
315B ILE* 2.9 17.8 + - + +
316B GLY* 3.7 4.7 - - - +
318B THR* 1.3 73.4 - - - +
320B ASN* 1.4 61.8 + - - +
322B VAL* 3.0 9.4 + - + +
323B PHE* 2.8 53.4 + - + -
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Residues in contact with ASN 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ALA* 3.9 25.1 + - - +
167B HIS* 5.0 9.8 + - - +
316B GLY 2.9 22.8 + - - +
317B ASP* 3.1 17.5 + - - +
319B LEU* 1.4 75.7 - - - +
321B GLN* 1.4 59.5 + - + +
323B PHE* 3.3 9.4 + - - +
324B GLU* 3.0 27.7 + - - +
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Residues in contact with GLN 321 (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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317B ASP* 2.8 39.1 + - - +
318B THR 3.0 8.7 + - - +
320B ASN* 1.4 75.5 - - + +
322B VAL* 1.3 64.1 + - - +
324B GLU* 3.3 16.7 + - - +
325B ILE* 3.1 31.0 + - + +
340B LEU* 4.0 22.2 - - + +
344B ARG* 3.2 27.2 + - - +
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B PRO* 4.4 9.2 - - + -
286B VAL* 4.4 10.8 - - + -
318B THR 3.0 18.6 + - - +
319B LEU* 3.4 14.1 - - + +
321B GLN* 1.3 76.6 - - - +
323B PHE* 1.3 71.9 + - + +
325B ILE* 3.3 5.3 + - - -
326B SER* 2.9 18.4 + - - -
333B PRO* 3.6 31.0 - - + +
336B ALA* 3.4 9.4 - - + +
337B ALA* 3.9 25.8 - - + +
340B LEU* 3.7 18.6 - - + -
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Residues in contact with PHE 323 (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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163B ALA 4.4 1.6 - - - -
164B THR* 3.5 48.7 - - + -
167B HIS* 3.5 38.1 - + + +
280B LEU* 3.8 22.9 - - + -
281B TYR 3.6 21.8 - - - -
282B ALA* 4.3 0.7 - - - -
283B PRO* 4.7 0.4 - - + -
319B LEU* 2.8 48.9 + - + +
320B ASN* 4.0 7.4 - - - +
322B VAL* 1.3 82.8 - - + +
324B GLU* 1.3 56.9 + - - +
326B SER* 3.5 5.3 - - - -
327B ASP* 2.8 37.1 + - - +
333B PRO* 4.3 10.3 - - + -
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Residues in contact with GLU 324 (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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167B HIS* 5.0 2.8 - - - -
320B ASN 3.0 13.2 + - - +
321B GLN* 3.5 20.5 - - - +
322B VAL 3.2 0.2 - - - -
323B PHE* 1.3 77.1 - - - +
325B ILE* 1.4 55.3 + - + +
327B ASP* 3.4 6.6 + - - +
328B ASN* 2.8 59.0 + - - +
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Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B GLN* 3.1 17.2 + - + +
322B VAL* 3.6 6.7 - - - +
324B GLU* 1.4 77.3 - - + +
326B SER* 1.4 58.7 + - - +
328B ASN* 4.5 5.8 - - - +
329B ASP* 2.8 48.7 + - - +
331B VAL* 4.6 4.3 - - + -
336B ALA* 3.7 24.2 - - + +
339B THR* 4.3 11.4 - - + -
340B LEU* 4.0 33.7 - - + +
343B ARG* 3.5 32.5 - - - +
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Residues in contact with SER 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B HIS* 4.0 9.1 - - - -
280B LEU* 5.8 1.3 - - - +
322B VAL 2.9 14.5 + - - -
323B PHE* 3.5 12.8 - - - -
325B ILE* 1.4 75.7 - - - +
327B ASP* 1.3 60.5 + - - +
330B GLY* 2.9 25.3 + - - -
331B VAL* 2.6 33.2 + - - +
332B THR 3.8 7.1 - - - -
333B PRO* 3.8 14.4 - - - +
336B ALA* 3.6 13.6 - - - +
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Residues in contact with ASP 327 (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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167B HIS* 2.9 34.3 + - - -
275B HIS* 6.2 0.3 - - - -
323B PHE* 2.8 19.0 + - - +
324B GLU* 3.7 5.0 - - - +
326B SER* 1.3 78.3 + - - +
328B ASN* 1.3 68.3 + - - +
330B GLY* 3.7 5.4 + - - -
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Residues in contact with ASN 328 (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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324B GLU* 2.8 46.7 + - - +
325B ILE* 4.0 4.2 - - - +
327B ASP* 1.3 81.0 - - - +
329B ASP* 1.3 68.9 + - - +
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Residues in contact with ASP 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ILE* 2.8 35.0 + - - +
328B ASN* 1.3 82.9 - - - +
330B GLY* 1.3 65.5 + - - +
331B VAL* 3.8 19.9 - - + +
339B THR* 5.3 1.9 - - - +
343B ARG* 4.1 12.1 + - - -
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Residues in contact with GLY 330 (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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275B HIS* 5.0 7.1 + - - -
326B SER 2.9 11.9 + - - -
327B ASP 3.7 4.5 + - - -
328B ASN 3.5 3.0 + - - -
329B ASP* 1.3 81.6 - - - +
331B VAL* 1.3 62.2 + - - +
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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
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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