Contacts of the helix formed by residues 312 - 325 (chain A) in PDB entry 3KTC
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 ASN 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A ALA* 2.9 12.2 + - - +
310A ALA* 4.2 10.1 - - + +
311A GLN* 1.3 73.4 - - - +
313A PRO* 1.3 64.1 - - - +
314A LEU* 2.9 25.3 + - - +
315A GLN* 3.0 48.4 + - - +
316A ALA* 3.1 26.4 + - - +
90B ARG* 4.6 1.8 - - - +
137B GLN* 4.4 1.3 + - - -
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Residues in contact with PRO 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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311A GLN 3.2 11.6 - - - +
312A ASN* 1.3 85.1 - - - +
314A LEU* 1.3 71.8 + - + +
316A ALA* 3.8 6.2 - - + +
317A GLN* 2.9 34.5 + - - +
90B ARG* 5.3 1.1 - - - +
134B TYR* 3.3 46.9 - - + -
137B GLN* 3.5 25.1 - - + +
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Residues in contact with LEU 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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312A ASN* 2.9 11.3 + - - +
313A PRO* 1.3 87.6 - - + +
315A GLN* 1.3 61.6 + - + +
317A GLN* 3.9 3.6 - - - +
318A ARG* 2.9 30.9 + - - +
134B TYR* 4.8 15.7 - - + +
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Residues in contact with GLN 315 (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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306A ALA 5.3 0.3 - - - -
307A ALA* 3.7 24.4 - - + +
310A ALA* 4.8 4.5 - - - +
312A ASN* 3.0 40.4 + - - +
314A LEU* 1.3 75.7 - - + +
316A ALA* 1.3 65.5 + - - +
318A ARG* 3.3 7.7 + - - +
319A ILE* 3.1 32.7 + - + +
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Residues in contact with ALA 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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304A LEU* 3.7 14.7 - - + +
307A ALA* 3.6 12.5 - - + +
308A GLN* 4.8 1.6 - - + -
312A ASN 3.1 17.8 + - - +
313A PRO* 3.9 6.3 - - + +
315A GLN* 1.3 77.3 - - - +
317A GLN* 1.3 58.7 + - + +
319A ILE* 3.3 4.1 + - - +
320A VAL* 3.0 33.3 + - - +
136B PHE* 3.4 31.6 - - + +
137B GLN* 4.4 1.6 - - - +
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Residues in contact with GLN 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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249A THR* 3.9 27.0 + - - +
313A PRO* 2.9 22.1 + - + +
314A LEU* 4.0 4.0 - - - +
316A ALA* 1.3 73.2 - - + +
318A ARG* 1.3 60.3 + - - +
320A VAL* 3.7 7.9 - - - +
321A GLN* 2.8 59.9 + - - +
134B TYR* 4.5 18.4 - - + +
135B PRO* 3.0 37.9 + - - +
136B PHE* 4.8 1.6 - - - +
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Residues in contact with ARG 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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314A LEU 2.9 19.2 + - - +
315A GLN* 3.3 8.0 + - - +
317A GLN* 1.3 75.8 - - - +
319A ILE* 1.3 63.4 + - + +
321A GLN* 3.6 10.5 + - - +
322A ASP* 3.1 43.1 + - - +
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Residues in contact with ILE 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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299A LEU* 3.9 16.3 - - + +
300A ASP* 3.7 32.5 + - + +
303A ALA* 3.5 39.5 - - + +
304A LEU* 3.7 11.0 - - + +
307A ALA* 4.4 3.1 - - + -
315A GLN* 3.1 23.8 + - + +
316A ALA* 3.6 6.1 - - - +
318A ARG* 1.3 77.1 - - + +
320A VAL* 1.3 64.3 + - - +
322A ASP* 3.4 9.7 + - - +
323A ALA* 3.4 15.9 + - - +
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Residues in contact with VAL 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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249A THR* 4.6 10.8 - - + +
252A PHE* 3.8 12.9 - - + -
299A LEU* 4.1 13.0 - - + -
304A LEU* 4.1 8.1 - - + -
316A ALA 3.0 20.2 + - - +
317A GLN* 3.8 10.5 - - - +
319A ILE* 1.3 75.4 - - - +
321A GLN* 1.3 61.8 + - + +
323A ALA* 3.1 4.3 + - - +
324A LEU* 2.8 32.8 + - + +
136B PHE* 3.5 59.0 - - + -
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Residues in contact with GLN 321 (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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317A GLN* 2.8 45.9 + - - +
318A ARG* 3.9 10.9 - - - +
320A VAL* 1.3 75.0 - - + +
322A ASP* 1.3 59.5 + - - +
324A LEU* 4.5 2.5 - - - +
325A LEU* 2.8 60.6 + - + +
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Residues in contact with ASP 322 (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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298A LYS* 5.5 1.0 - - - +
318A ARG* 3.1 32.8 + - - +
319A ILE* 3.6 9.3 - - - +
320A VAL 3.2 0.2 - - - -
321A GLN* 1.3 78.8 - - - +
323A ALA* 1.3 60.2 + - - +
325A LEU 3.6 12.8 - - - +
326A SER* 4.2 4.9 - - - -
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Residues in contact with ALA 323 (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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252A PHE* 4.1 3.8 - - + -
295A ALA* 3.4 31.0 - - - +
298A LYS* 4.2 10.2 - - - +
299A LEU* 3.6 33.7 - - + +
319A ILE 3.4 2.1 + - - +
320A VAL 3.1 7.4 + - - +
322A ASP* 1.3 80.4 - - - +
324A LEU* 1.3 56.3 + - - +
325A LEU 3.4 0.2 - - - -
326A SER* 2.5 30.0 + - - -
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Residues in contact with LEU 324 (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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248A MSE 3.9 19.1 - - + +
249A THR* 3.9 35.2 - - - +
252A PHE* 4.0 21.3 - - + -
288A PHE* 5.1 2.0 - - + -
291A HIS* 2.7 38.6 + - + +
292A ILE* 3.9 27.6 - - + -
295A ALA* 4.0 4.9 - - + -
320A VAL* 2.8 23.7 + - + +
321A GLN* 4.4 3.4 - - - +
323A ALA* 1.3 69.4 - - - +
325A LEU* 1.3 69.3 + - + +
326A SER 3.1 8.2 + - - +
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Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A MSE 5.5 11.2 - - + -
321A GLN* 2.8 44.1 + - + +
322A ASP* 3.6 11.0 - - - +
324A LEU* 1.3 87.4 - - + +
326A SER* 1.3 60.8 + - - +
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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
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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