Contacts of the helix formed by residues 296 - 310 (chain A) in PDB entry 3KK3
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 THR 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A GLN* 4.8 2.5 - - - +
282A LEU* 3.0 31.9 - - + +
294A PRO 3.1 6.4 + - - -
295A LEU* 1.3 79.8 - - - +
297A GLU* 1.3 52.8 + - - +
298A GLU* 3.0 35.2 - - + +
299A ALA 3.2 3.5 + - - +
300A GLU* 2.7 30.5 + - - -
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Residues in contact with GLU 297 (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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295A LEU 3.5 3.5 + - - +
296A THR* 1.3 74.9 - - - +
298A GLU* 1.3 61.3 + - + +
300A GLU* 3.1 19.6 - - + +
301A LEU* 3.0 22.3 + - - +
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Residues in contact with GLU 298 (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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278A GLN* 3.4 31.9 + - - +
296A THR* 3.0 13.9 - - + -
297A GLU* 1.3 78.5 - - + +
299A ALA* 1.3 64.9 + - - +
301A LEU* 3.0 26.4 + - - +
302A GLU* 3.1 11.4 + - - +
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Residues in contact with ALA 299 (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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278A GLN* 3.8 22.6 + - - +
279A LEU* 3.9 15.2 - - + +
282A LEU* 3.7 20.9 - - + -
295A LEU* 3.6 14.1 - - + -
296A THR* 3.2 13.6 + - - +
298A GLU* 1.3 77.6 - - - +
300A GLU* 1.3 55.9 + - - +
302A GLU* 2.6 23.8 + - - +
303A LEU* 2.8 16.3 + - - +
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Residues in contact with GLU 300 (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 TRP* 4.9 3.1 - - - -
295A LEU* 2.8 39.7 - - + +
296A THR 2.7 11.7 + - - +
297A GLU* 3.1 29.4 - - + +
299A ALA* 1.3 72.0 - - - +
301A LEU* 1.3 64.2 + - - +
303A LEU* 4.4 16.6 - - - +
304A ALA* 3.2 21.7 + - - +
307A ARG* 5.7 0.7 + - - -
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Residues in contact with LEU 301 (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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297A GLU 3.0 13.7 + - - +
298A GLU* 3.0 22.0 + - - +
300A GLU* 1.3 77.2 - - - +
302A GLU* 1.3 65.7 + - + +
304A ALA* 3.2 5.5 + - - +
305A GLU* 2.9 48.6 + - + +
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Residues in contact with GLU 302 (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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275A LYS* 2.9 43.3 - - + +
276A VAL* 3.3 8.5 - - - -
278A GLN* 2.5 45.6 + - + +
279A LEU* 3.3 13.1 - - + +
298A GLU 3.1 4.1 + - - +
299A ALA* 2.6 16.5 + - - +
301A LEU* 1.3 72.9 - - + +
303A LEU* 1.3 68.7 + - - +
305A GLU* 2.8 28.3 + - - +
306A ASN* 2.8 15.1 + - - -
336A GLN* 2.9 16.5 + - - +
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Residues in contact with LEU 303 (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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246A LEU* 4.2 17.0 - - + -
252A TRP* 4.2 19.7 - - + -
260A LEU* 4.3 22.7 - - + -
264A LEU* 5.4 1.8 - - + -
279A LEU* 4.1 14.6 - - + +
295A LEU* 4.8 6.3 - - + -
299A ALA 2.8 17.9 + - - +
300A GLU* 4.2 20.2 - - - +
302A GLU* 1.3 72.7 - - - +
304A ALA* 1.3 54.8 + - - +
306A ASN* 3.0 10.3 + - + +
307A ARG* 2.7 75.5 + - - +
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Residues in contact with ALA 304 (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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300A GLU* 3.2 15.1 + - - +
301A LEU* 3.3 11.2 - - - +
302A GLU 3.1 0.4 - - - -
303A LEU* 1.3 80.0 - - - +
305A GLU* 1.3 63.3 + - - +
307A ARG* 3.3 7.4 + - - +
308A GLU* 3.1 30.7 + - + +
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Residues in contact with GLU 305 (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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275A LYS* 2.8 47.1 + - + +
301A LEU* 2.9 38.1 + - + +
302A GLU* 2.8 21.7 + - - +
304A ALA* 1.3 72.2 - - - +
306A ASN* 1.3 62.8 + - - +
308A GLU* 3.5 6.6 - - - +
309A ILE* 3.1 27.9 + - + +
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Residues in contact with ASN 306 (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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246A LEU* 5.1 2.0 - - + -
264A LEU* 3.8 33.8 - - + +
273A GLY 4.2 3.4 + - - -
274A ILE* 3.5 15.3 - - + +
275A LYS* 2.7 49.5 - - - +
279A LEU* 4.7 1.4 - - - +
302A GLU* 2.8 20.3 + - - +
303A LEU* 3.4 10.2 - - + +
305A GLU* 1.3 72.8 - - - +
307A ARG* 1.3 60.5 + - - +
308A GLU 2.8 1.6 - - - -
309A ILE* 2.6 29.4 + - - +
310A LEU* 2.9 14.9 + - - +
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Residues in contact with ARG 307 (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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246A LEU* 4.3 29.3 + - + +
247A PRO 4.3 4.0 + - - -
248A GLU* 3.5 48.6 + - - +
252A TRP* 4.6 7.5 - - - -
260A LEU* 5.6 0.2 - - - +
300A GLU* 5.7 0.6 + - - -
303A LEU* 2.7 57.4 + - + +
304A ALA* 3.9 7.2 - - - +
306A ASN* 1.3 72.6 - - - +
308A GLU* 1.3 59.1 + - + +
310A LEU* 3.5 13.9 + - + +
311A LYS* 3.3 37.5 - - - +
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Residues in contact with GLU 308 (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 ALA* 3.1 20.3 + - + +
305A GLU* 3.5 7.2 - - - +
306A ASN 2.8 1.0 + - - -
307A ARG* 1.3 75.4 - - + +
309A ILE* 1.3 65.5 + - + +
310A LEU 3.1 2.7 + - - -
311A LYS* 3.1 47.3 + - - +
312A GLU* 4.2 5.4 + - - +
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Residues in contact with ILE 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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271A TYR* 4.1 22.9 - - + -
272A PRO* 3.7 18.2 - - + +
273A GLY* 3.4 34.8 - - - +
274A ILE* 4.3 6.1 - - + +
305A GLU* 3.2 18.6 - - + +
306A ASN* 2.6 19.5 + - - +
308A GLU* 1.3 73.9 - - + +
310A LEU* 1.3 56.6 + - - +
312A GLU* 3.0 34.2 + - + +
314A VAL* 6.1 0.4 - - + -
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Residues in contact with LEU 310 (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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244A ILE* 4.5 21.1 - - + +
246A LEU* 3.5 44.6 - - + +
264A LEU* 4.8 3.1 - - + -
267A ALA* 4.2 13.2 - - + -
271A TYR* 3.6 45.8 + - + +
274A ILE* 4.8 7.9 - - + -
306A ASN 2.9 11.6 + - - +
307A ARG* 3.6 12.3 - - + +
308A GLU 3.1 0.6 - - - -
309A ILE* 1.3 74.3 - - - +
311A LYS* 1.3 60.3 + - + +
312A GLU 3.1 13.1 + - - +
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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
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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