Contacts of the helix formed by residues 301 - 314 (chain S) in PDB entry 5L4K
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 GLU 301 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296S LYS* 3.4 47.3 + - + +
299S GLN* 3.9 19.2 + - + +
300S LEU* 1.3 83.2 - - - +
302S TYR* 1.3 58.5 + - - +
303S SER* 2.6 25.1 + - - +
304S GLU* 3.3 30.4 + - - +
305S ALA* 3.7 5.5 + - - +
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Residues in contact with TYR 302 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296S LYS 5.3 0.2 - - - -
297S ALA* 4.3 9.6 - - + +
300S LEU* 3.0 37.9 - - + +
301S GLU* 1.3 74.0 - - - +
303S SER* 1.3 65.7 + - - +
305S ALA* 3.2 9.7 + - - +
306S ARG* 3.0 19.6 + - - +
335S VAL* 4.2 10.9 - - + +
338S LEU* 3.1 61.5 - - + +
339S LEU* 3.6 30.0 - - + +
397S ARG* 3.7 17.1 + - - +
400S HIS* 6.0 0.2 + - - -
404S LYS* 6.3 1.3 - - - -
237T MET* 3.8 14.4 - - + +
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Residues in contact with SER 303 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301S GLU* 2.6 14.2 + - - +
302S TYR* 1.3 74.9 + - - +
304S GLU* 1.3 69.9 + - - +
306S ARG* 3.5 8.1 + - - +
307S ARG* 3.9 7.8 + - - +
339S LEU* 4.3 10.6 - - - +
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Residues in contact with GLU 304 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296S LYS* 3.1 44.0 + - + +
301S GLU* 3.3 25.4 + - - +
303S SER* 1.3 82.6 - - - +
305S ALA* 1.3 65.0 + - - +
307S ARG* 3.0 42.8 + - - +
308S THR* 3.0 17.3 + - - +
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Residues in contact with ALA 305 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293S GLY* 4.1 20.6 - - - +
296S LYS* 4.4 6.6 - - + +
297S ALA* 4.3 17.0 - - + +
301S GLU 3.7 4.4 + - - +
302S TYR* 3.5 17.5 - - - +
303S SER 3.1 0.8 - - - -
304S GLU* 1.3 77.7 - - - +
306S ARG* 1.3 66.1 + - - +
307S ARG 2.7 1.9 + - - -
308S THR* 2.8 17.2 + - - +
309S MET* 2.8 19.5 + - + +
335S VAL* 4.8 10.1 - - + -
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Residues in contact with ARG 306 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302S TYR 3.0 8.2 + - - +
303S SER 4.1 2.0 - - - +
304S GLU 3.4 0.2 - - - -
305S ALA* 1.3 76.8 - - - +
307S ARG* 1.3 53.3 + - - +
309S MET* 4.3 2.1 - - - +
310S THR* 2.6 30.3 + - - +
332S LEU* 4.6 4.0 - - + -
335S VAL* 4.2 17.9 - - + +
336S GLU* 3.4 46.9 + - + +
339S LEU* 3.7 34.7 - - + +
341S GLU* 4.0 29.4 + - - -
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Residues in contact with ARG 307 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303S SER 3.9 4.3 + - - +
304S GLU* 3.0 39.2 + - - +
305S ALA 2.7 5.7 + - - -
306S ARG* 1.3 75.8 - - - +
308S THR* 1.3 72.3 + - - +
310S THR* 4.1 4.2 + - - -
311S ASN* 2.6 42.2 + - - +
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Residues in contact with THR 308 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289S LEU* 3.3 46.7 - - + +
292S THR* 3.7 14.9 - - + +
293S GLY* 4.6 9.0 - - - +
296S LYS* 5.8 2.1 - - - +
304S GLU* 3.0 13.2 + - - +
305S ALA* 2.8 11.3 + - - -
307S ARG* 1.3 85.3 + - - +
309S MET* 1.3 66.4 + - - -
310S THR 3.0 2.0 + - - -
311S ASN* 3.0 8.3 + - - +
312S ALA* 2.9 20.3 + - - +
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Residues in contact with MET 309 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289S LEU 4.4 3.3 + - - +
290S TYR* 4.4 15.5 - - - +
293S GLY* 4.1 24.9 - - - +
294S ARG 4.3 0.7 - - - +
297S ALA* 5.2 0.2 - - + -
305S ALA* 2.8 22.4 + - + +
306S ARG* 4.3 2.0 - - - +
308S THR* 1.3 72.8 - - - +
310S THR* 1.3 61.6 + - - +
312S ALA* 3.1 10.1 - - - +
313S LEU* 3.1 20.4 + - - +
328S VAL* 4.2 9.8 - - + +
331S LEU* 3.3 48.5 - - + -
332S LEU* 3.7 37.9 - - + -
335S VAL* 4.1 13.5 - - + -
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Residues in contact with THR 310 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306S ARG* 2.6 27.1 + - - +
307S ARG* 4.3 4.5 - - - -
308S THR 3.1 0.8 - - - -
309S MET* 1.3 75.1 - - - +
311S ASN* 1.3 69.2 + - - +
312S ALA 3.0 0.7 + - - -
313S LEU* 3.0 19.7 + - + +
314S ARG* 3.2 47.2 + - + +
332S LEU* 3.7 21.7 - - + +
336S GLU* 5.5 0.3 + - - -
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Residues in contact with ASN 311 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381R GLN* 5.7 5.7 - - - +
289S LEU* 4.3 16.9 - - + +
307S ARG* 2.6 29.4 + - - +
308S THR* 3.0 9.5 + - - +
310S THR* 1.3 78.3 - - - +
312S ALA* 1.3 64.9 + - - +
314S ARG* 3.2 19.5 + - - +
315S LYS* 3.3 21.5 + - + +
482S PHE* 6.4 0.2 - - - -
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Residues in contact with ALA 312 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286S ALA* 4.3 11.4 - - - +
289S LEU* 4.0 33.3 - - + +
290S TYR* 4.1 10.8 - - + +
308S THR 2.9 11.6 + - - +
309S MET* 3.1 12.8 - - - +
310S THR 3.0 0.2 - - - -
311S ASN* 1.3 73.6 - - - +
313S LEU* 1.3 69.4 + - - +
314S ARG 2.8 1.6 + - - -
315S LYS* 2.9 15.1 + - - +
316S ALA* 3.5 9.2 + - - +
324S PHE* 4.9 7.2 - - + -
328S VAL* 5.1 4.0 - - + -
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Residues in contact with LEU 313 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309S MET 3.1 7.1 + - - +
310S THR* 3.0 14.4 + - + +
312S ALA* 1.3 78.6 - - - +
314S ARG* 1.3 65.3 + - + +
315S LYS 3.5 0.7 + - - -
316S ALA* 3.9 6.2 + - - +
324S PHE* 5.7 0.7 - - - -
325S LYS* 3.7 39.9 - - + -
328S VAL* 3.4 29.5 - - + +
329S HIS* 3.3 42.8 - - + +
332S LEU* 4.2 15.5 - - + -
347S GLN* 6.0 0.7 - - + +
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Residues in contact with ARG 314 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378R ASN* 3.8 31.7 + - - +
381R GLN* 3.5 36.0 - - - +
382R LYS* 5.3 24.1 - - + +
385R ARG* 3.8 25.7 + - + +
310S THR* 3.2 36.9 + - - +
311S ASN* 3.2 15.6 + - - +
312S ALA 2.8 1.4 + - - -
313S LEU* 1.3 84.8 - - + +
315S LYS* 1.3 60.3 + - - +
316S ALA 3.8 2.5 - - - -
318S GLN* 4.7 5.9 + - - +
482S PHE* 5.6 3.6 - - - -
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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