Contacts of the helix formed by residues 316 - 330 (chain A) in PDB entry 2KTY
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 LEU 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A LEU* 4.5 1.4 - - - +
305A THR* 4.6 9.9 - - + +
309A LEU* 3.8 31.6 - - + -
314A LYS 4.3 2.9 - - - +
315A PRO* 1.3 84.7 - - - +
317A TYR* 1.3 56.6 + - - +
318A GLU* 3.3 25.4 - - + +
319A ASN* 3.7 22.2 - - + +
320A LEU* 2.7 50.5 + - + +
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Residues in contact with TYR 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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162A LEU* 3.7 33.3 - - + +
163A ASP* 6.1 0.4 - - - -
165A LEU* 4.8 8.2 - - + +
166A GLU* 3.1 48.8 - - + +
169A HIS* 4.5 13.3 - - - -
240A ARG* 5.1 3.1 - - - +
244A LEU* 4.9 7.0 - - + -
315A PRO* 3.5 33.6 - - + +
316A LEU* 1.3 72.0 - - - +
318A GLU* 1.3 55.4 + - - +
320A LEU* 3.9 5.3 - - - +
321A ARG* 2.7 51.1 + - - +
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 3.6 13.9 - - + +
317A TYR* 1.3 82.4 - - - +
319A ASN* 1.3 92.0 + - - +
321A ARG* 3.8 6.6 - - - +
322A ASP* 2.9 41.4 + - - +
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Residues in contact with ASN 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A THR* 4.8 14.1 + - + +
316A LEU* 3.4 31.9 + - + +
317A TYR 3.4 0.2 - - - -
318A GLU* 1.3 102.3 + - - +
320A LEU* 1.3 62.3 + - + +
322A ASP* 3.1 8.1 + - - +
323A ILE* 3.0 27.5 + - - +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 5.0 4.7 - - + -
244A LEU* 3.2 42.6 - - + -
302A TYR* 3.2 45.6 - - + +
305A THR* 3.8 12.3 - - + -
306A VAL* 3.5 20.0 - - + -
316A LEU* 2.7 42.0 + - + +
317A TYR* 3.9 4.7 - - - +
319A ASN* 1.3 72.1 - - - +
321A ARG* 1.3 62.3 + - - +
323A ILE* 2.8 25.3 - - - +
324A LEU* 2.9 12.8 + - - +
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Residues in contact with ARG 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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104A LYS 5.5 5.5 + - - -
106A LYS* 4.8 8.7 - - - +
159A LEU* 3.9 21.5 + - + +
162A LEU* 5.7 7.1 - - + +
163A ASP* 3.0 36.1 + - - +
317A TYR* 2.7 35.4 + - - +
318A GLU* 3.9 5.2 - - - +
320A LEU* 1.3 73.9 - - - +
322A ASP* 1.3 59.3 + - - +
324A LEU* 4.3 7.0 - - - -
325A LEU* 3.0 51.5 + - + +
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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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318A GLU* 2.9 28.1 + - - +
319A ASN* 3.2 9.4 - - - +
320A LEU 3.1 0.2 - - - -
321A ARG* 1.3 78.6 - - - +
323A ILE* 1.3 56.1 + - - +
325A LEU* 3.3 3.3 + - - +
326A GLN* 2.7 38.6 + - - +
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Residues in contact with ILE 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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297A GLY 5.6 0.2 - - - -
298A GLU* 2.9 36.1 - - - +
301A LYS* 3.3 34.1 - - + -
302A TYR* 3.3 13.7 - - + +
305A THR* 5.7 4.9 - - - +
319A ASN* 3.0 13.9 + - - +
320A LEU* 2.8 30.7 - - + +
322A ASP* 1.3 77.0 - - - +
324A LEU* 1.3 57.2 - - - +
326A GLN* 3.6 6.7 - - + +
327A GLY* 3.0 26.0 + - - -
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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
----------------------------------------------------------
155A LEU* 3.5 36.8 - - + +
158A SER* 3.4 26.7 - - - +
159A LEU* 4.9 7.4 - - + -
162A LEU* 4.9 3.4 - - + -
251A MET* 3.6 22.7 - - + -
298A GLU* 3.5 32.2 - - + +
302A TYR* 3.7 23.6 - - + -
320A LEU 2.9 15.3 + - - +
321A ARG* 3.8 6.5 - - - +
323A ILE* 1.3 79.7 - - - +
325A LEU* 1.3 57.8 + - - +
328A LEU* 3.0 30.8 + - - +
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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
----------------------------------------------------------
155A LEU* 4.9 3.8 - - + -
159A LEU* 4.2 22.9 - - + -
321A ARG* 3.0 50.2 + - + +
322A ASP* 3.9 3.1 - - - +
324A LEU* 1.3 75.1 - - - +
326A GLN* 1.3 58.8 + - - +
328A LEU* 4.4 6.9 - - + +
329A LYS* 2.9 39.0 + - + +
334A LYS* 5.3 17.9 - - + -
335A ASP* 5.7 4.5 - - - +
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Residues in contact with GLN 326 (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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322A ASP 2.7 19.1 + - - +
323A ILE* 3.6 9.4 - - - +
325A LEU* 1.3 78.2 - - - +
327A GLY* 1.3 55.7 + - - +
329A LYS* 4.8 13.3 - - - +
330A ALA* 2.7 43.1 + - + +
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Residues in contact with GLY 327 (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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151A ARG* 4.3 0.3 + - - -
295A LYS* 6.0 0.5 - - - +
298A GLU* 3.2 30.9 - - - +
323A ILE 3.0 12.7 + - - -
326A GLN* 1.3 76.5 - - - +
328A LEU* 1.3 63.2 + - - +
330A ALA* 3.5 16.7 - - - +
331A ILE* 4.0 9.7 + - - +
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Residues in contact with LEU 328 (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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151A ARG* 3.6 40.6 - - + -
152A LYS* 4.2 7.4 - - + +
155A LEU* 3.6 30.1 - - + -
298A GLU* 3.4 5.2 - - - +
324A LEU 3.0 18.9 + - - +
325A LEU* 4.2 6.1 - - + +
327A GLY* 1.3 76.5 - - - +
329A LYS* 1.3 54.2 + - + +
331A ILE* 3.0 24.8 - - + +
333A SER* 2.6 44.8 - - - +
334A LYS* 3.4 23.1 - - + -
335A ASP* 5.0 1.3 - - - +
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Residues in contact with LYS 329 (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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325A LEU* 2.9 28.6 + - + +
326A GLN* 4.3 12.5 - - - +
328A LEU* 1.3 74.4 - - - +
330A ALA* 1.3 56.5 + - - +
331A ILE 3.0 3.4 - - - -
332A GLY* 2.7 26.0 + - - -
333A SER 3.4 8.1 - - - +
334A LYS* 3.4 39.9 - - + +
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Residues in contact with ALA 330 (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 LYS* 5.7 7.4 - - - -
326A GLN* 2.7 31.7 + - + +
327A GLY* 3.5 14.1 - - - +
328A LEU 3.3 0.6 - - - -
329A LYS* 1.3 78.6 - - - +
331A ILE* 1.3 59.6 + - + +
332A GLY 3.1 3.3 + - - -
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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