Contacts of the helix formed by residues 320 - 339 (chain A) in PDB entry 1K4S
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 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A GLN 3.6 2.9 + - - -
319A MET* 1.3 72.5 - - - +
321A LYS* 1.3 58.3 + - - +
322A GLU* 3.1 17.2 + - - +
323A GLU* 3.1 21.0 + - - +
324A LYS* 2.7 37.5 + - - +
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Residues in contact with LYS 321 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A MET 3.7 1.4 + - - -
320A SER* 1.3 71.9 + - - +
322A GLU* 1.3 53.6 + - - +
324A LYS* 3.5 17.2 + - - +
325A LEU* 2.5 39.7 + - - +
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Residues in contact with GLU 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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320A SER* 3.1 7.5 + - - +
321A LYS* 1.3 78.9 - - - +
323A GLU* 1.3 67.2 + - - +
325A LEU* 3.2 18.2 + - + +
326A LYS* 3.1 20.6 + - - +
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Residues in contact with GLU 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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319A MET* 4.8 3.4 - - + -
320A SER* 3.1 31.5 + - - +
322A GLU* 1.3 81.3 - - - +
324A LYS* 1.3 61.8 + - + +
326A LYS* 3.3 16.7 - - - +
327A ILE* 3.7 7.9 - - - +
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Residues in contact with LYS 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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316A ARG 4.5 7.0 - - - +
319A MET* 3.1 44.9 - - + +
320A SER 2.7 21.7 + - - +
321A LYS* 3.5 19.2 + - - +
323A GLU* 1.3 67.4 - - - +
325A LEU* 1.3 56.5 + - - +
326A LYS 3.0 2.5 - - - -
327A ILE* 2.6 46.9 + - + +
328A LYS* 2.8 12.8 + - + -
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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
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321A LYS 2.5 23.6 + - - +
322A GLU* 3.2 18.2 - - + +
324A LYS* 1.3 72.4 - - - +
326A LYS* 1.3 67.9 + - - +
328A LYS* 3.0 21.7 + - + +
329A GLU* 2.9 44.6 + - + +
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Residues in contact with LYS 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 GLU 3.1 7.5 + - - +
323A GLU* 3.3 14.1 - - - +
324A LYS 3.0 0.2 - - - -
325A LEU* 1.3 77.6 - - - +
327A ILE* 1.3 54.1 + - + +
329A GLU* 2.6 25.1 - - - +
330A GLU* 2.7 33.8 + - - +
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Residues in contact with ILE 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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323A GLU 3.7 12.8 - - - +
324A LYS* 2.6 32.4 + - + +
326A LYS* 1.3 74.3 - - + +
328A LYS* 1.3 57.2 - - + +
330A GLU* 3.2 28.5 + - - +
331A ASN* 2.4 54.4 + - - +
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Residues in contact with LYS 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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324A LYS* 2.8 14.1 + - + +
325A LEU* 3.2 22.9 - - + +
327A ILE* 1.3 77.5 - - + +
329A GLU* 1.3 93.6 + - + +
331A ASN* 3.2 7.4 + - - +
332A GLU* 3.0 36.9 + - - +
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Residues in contact with GLU 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 43.5 + - + +
326A LYS* 2.6 28.2 - - - +
328A LYS* 1.3 95.1 - - + +
330A GLU* 1.3 65.3 + - - +
332A GLU* 2.9 5.6 + - - +
333A LYS* 2.8 21.3 + - - +
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Residues in contact with GLU 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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326A LYS* 2.7 19.1 + - - +
327A ILE* 3.1 30.0 + - - +
329A GLU* 1.3 76.7 + - - +
331A ASN* 1.3 81.7 + - - +
333A LYS* 2.9 26.3 + - - +
334A LEU* 3.5 3.5 + - - +
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Residues in contact with ASN 331 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A ILE* 2.4 50.7 + - - +
328A LYS* 3.5 6.8 + - - +
330A GLU* 1.3 95.5 + - - +
332A GLU* 1.3 62.7 + - - +
334A LEU* 3.2 27.6 - - + +
335A LEU* 3.9 7.6 + - - +
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Residues in contact with GLU 332 (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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328A LYS* 3.0 30.6 + - - +
329A GLU* 2.9 13.3 + - - +
331A ASN* 1.3 77.2 - - - +
333A LYS* 1.3 60.7 + - - +
335A LEU* 3.0 23.3 + - + +
336A LYS* 3.0 33.6 - - - +
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Residues in contact with LYS 333 (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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329A GLU 2.8 10.4 + - - +
330A GLU* 2.9 17.9 + - - +
332A GLU* 1.3 75.2 - - - +
334A LEU* 1.3 62.1 + - - +
335A LEU 3.2 0.9 + - - -
336A LYS* 3.2 21.3 + - - +
337A GLU* 3.6 10.2 + - - +
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Residues in contact with LEU 334 (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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226A VAL* 3.9 15.3 - - + -
330A GLU 3.5 3.4 + - - +
331A ASN* 3.2 20.6 + - + +
333A LYS* 1.3 79.4 - - - +
335A LEU* 1.3 53.1 + - + +
337A GLU* 3.2 4.6 + - - -
338A TYR* 2.6 76.4 + - + +
353A PHE* 3.4 27.8 - - + -
354A LYS* 4.3 15.5 - - + +
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Residues in contact with LEU 335 (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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331A ASN 3.9 9.0 - - - +
332A GLU* 3.1 26.7 - - + +
334A LEU* 1.3 75.0 - - + +
336A LYS* 1.3 70.2 + - - +
338A TYR 2.6 8.8 + - - -
339A GLY* 2.4 37.0 + - - +
340A PHE* 3.6 14.2 - - + -
349A ARG* 5.2 12.8 - - - +
353A PHE* 3.4 28.3 - - + -
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Residues in contact with LYS 336 (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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332A GLU* 3.0 44.0 + - - +
333A LYS* 3.2 10.4 + - - +
335A LEU* 1.3 94.5 - - - +
337A GLU* 1.3 58.7 + - + +
340A PHE* 4.0 20.7 + - + +
347A LYS* 3.7 22.2 + - - +
349A ARG* 5.9 0.9 - - - +
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Residues in contact with GLU 337 (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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223A LYS* 3.3 37.2 - - + +
333A LYS 3.6 6.1 + - - +
334A LEU* 3.2 5.9 + - - +
335A LEU 2.7 1.4 + - - -
336A LYS* 1.3 78.0 - - + +
338A TYR* 1.3 96.8 + - - +
339A GLY 3.9 0.2 - - - -
340A PHE 5.4 1.1 - - - -
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Residues in contact with TYR 338 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A LYS* 3.1 54.1 - - + +
224A GLY 4.1 9.9 - - - +
225A PRO 4.2 9.4 - - - -
226A VAL* 3.8 17.0 - - + -
334A LEU* 2.6 41.9 + - + +
335A LEU 2.6 10.1 + - - -
337A GLU* 1.3 101.0 + - - +
339A GLY* 1.3 51.4 + - - -
340A PHE 3.7 2.4 + - - -
350A ILE* 5.3 2.8 - - - +
353A PHE* 2.7 30.5 - - + +
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Residues in contact with GLY 339 (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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335A LEU* 2.4 26.6 + - - -
338A TYR* 1.3 68.6 - - - +
340A PHE* 1.3 71.9 + - - +
341A CYS 4.2 0.2 - - - -
349A ARG* 3.3 8.6 - - - +
350A ILE* 3.1 28.8 + - - -
353A PHE* 3.3 19.7 - - - -
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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