Contacts of the helix formed by residues 299 - 313 (chain B) in PDB entry 3LPK
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 LYS 299 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B LEU 3.4 0.2 + - - -
298B PRO* 1.3 69.6 - - - +
300B LYS* 1.3 64.6 + - - +
302B PHE* 3.3 1.6 + - - +
303B GLU* 3.0 61.0 + - - +
387B GLN* 3.7 38.4 - - + +
388B SER 3.2 13.1 + - - +
389B SER* 6.1 0.2 - - - -
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Residues in contact with LYS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B MET* 3.3 18.2 - - + +
280B GLU* 3.3 40.4 + - - +
298B PRO* 3.3 2.8 - - + +
299B LYS* 1.3 79.6 - - - +
301B VAL* 1.3 63.2 + - + +
303B GLU* 3.6 13.3 + - - +
304B ALA* 3.3 21.5 + - - +
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B VAL* 5.5 3.6 - - + -
274B LEU* 4.1 14.5 - - + +
276B MET* 3.8 15.9 - - + -
280B GLU* 3.4 35.0 - - + +
281B TYR* 3.9 26.0 - - + +
297B LEU* 4.3 22.2 - - + -
298B PRO* 2.8 21.8 + - + +
300B LYS* 1.3 71.2 - - + +
302B PHE* 1.3 61.2 + - - +
304B ALA* 3.2 1.7 + - - +
305B ALA* 2.8 29.5 + - + +
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU* 3.8 21.7 - - + +
298B PRO 2.8 15.6 + - - +
299B LYS* 3.5 8.3 - - - +
301B VAL* 1.3 73.3 - - - +
303B GLU* 1.3 64.5 + - + +
305B ALA* 3.7 0.9 - - - +
306B VAL* 2.9 63.1 + - + +
323B TRP 3.9 17.7 - - - -
324B LEU* 5.6 7.4 - - + -
383B PHE* 4.5 0.2 - + - -
385B ILE* 3.5 36.3 - - + -
386B SER* 3.5 20.0 - - - -
387B GLN* 3.9 33.7 - - + -
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B LYS* 3.0 50.1 + - + +
300B LYS* 3.9 13.6 - - - +
302B PHE* 1.3 85.4 - - + +
304B ALA* 1.3 63.2 + - - +
306B VAL* 4.0 4.1 - - - +
307B LYS* 3.1 42.3 + - - +
387B GLN* 5.1 3.8 - - - +
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 3.7 14.3 - - + +
276B MET* 3.9 22.0 - - + -
300B LYS 3.3 10.8 + - - +
301B VAL 3.2 7.7 + - - +
303B GLU* 1.3 77.5 - - - +
305B ALA* 1.3 64.2 + - - +
307B LYS* 3.4 11.4 + - - +
308B SER* 3.1 23.2 + - - -
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B VAL* 6.2 0.7 - - + -
269B ILE* 5.0 8.1 - - + -
274B LEU* 4.1 18.3 - - + +
297B LEU* 4.0 21.8 - - + -
301B VAL 2.8 19.9 + - - +
302B PHE* 3.7 3.6 - - + +
304B ALA* 1.3 74.5 - - - +
306B VAL* 1.3 59.2 + - + +
308B SER* 3.2 3.1 + - - -
309B ILE* 2.8 45.0 + - + +
344B ILE* 6.3 0.2 - - + -
385B ILE* 5.7 1.6 - - + -
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 2.9 57.9 + - + +
303B GLU* 4.0 4.3 - - - +
305B ALA* 1.3 73.6 - - + +
307B LYS* 1.3 62.5 + - + +
309B ILE* 3.8 7.0 - - + +
310B LYS* 2.8 60.4 + - + +
323B TRP* 4.1 16.8 - - + +
383B PHE* 4.2 13.7 - - + -
385B ILE* 5.6 0.7 - - + -
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Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B GLU* 3.1 31.4 + - - +
304B ALA* 3.7 8.5 - - - +
305B ALA 3.3 0.2 - - - -
306B VAL* 1.3 78.5 - - + +
308B SER* 1.3 58.4 + - - +
310B LYS* 3.6 9.5 - - + +
311B ALA* 3.0 27.4 + - - +
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ILE* 3.3 32.6 + - - +
272B GLN* 4.7 12.1 + - - +
274B LEU* 4.2 9.0 - - - +
304B ALA 3.1 17.6 + - - -
305B ALA 3.2 3.8 + - - -
307B LYS* 1.3 75.4 - - - +
309B ILE* 1.3 65.3 + - - +
311B ALA* 3.2 7.6 + - - +
312B ALA* 3.0 23.7 + - - +
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Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ILE* 4.2 18.4 - - + -
305B ALA* 2.8 34.7 + - + +
306B VAL* 3.9 4.0 - - + +
308B SER* 1.3 72.3 - - - +
310B LYS* 1.3 54.9 + - - +
312B ALA* 3.5 2.4 + - - +
313B SER* 2.7 33.6 + - - +
323B TRP* 3.6 24.2 - - + -
341B PHE* 4.7 4.7 - - + -
342B PRO* 4.1 24.5 - - + -
344B ILE* 3.9 24.5 - - + -
366B TYR* 4.4 7.6 - - + +
383B PHE* 4.0 14.6 - - + -
385B ILE* 4.0 15.9 - - + -
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Residues in contact with LYS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B VAL* 2.8 36.4 + - + +
307B LYS* 3.6 9.8 - - + +
309B ILE* 1.3 76.5 - - - +
311B ALA* 1.3 56.8 + - - +
313B SER* 3.2 7.7 + - - -
314B SER* 2.9 30.9 + - - -
320B ASP* 4.7 9.9 + - - -
323B TRP* 3.4 56.5 - - + +
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LYS 3.0 15.4 + - - +
308B SER* 3.2 11.2 + - - +
310B LYS* 1.3 77.7 - - - +
312B ALA* 1.3 61.1 + - - +
314B SER* 3.2 23.6 + - - -
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ILE* 4.9 2.7 - - + -
270B ASN* 4.5 9.4 + - + +
308B SER 3.0 16.3 + - - +
309B ILE 3.9 0.4 - - - +
310B LYS 3.3 0.2 - - - -
311B ALA* 1.3 78.2 - - - +
313B SER* 1.3 58.4 + - - +
314B SER* 3.4 1.5 + - - -
315B THR* 5.2 1.9 + - - +
340B ILE* 3.1 11.6 - - - +
342B PRO* 3.8 33.9 - - + -
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ILE 2.7 22.3 + - - -
310B LYS* 3.4 8.2 + - - -
312B ALA* 1.3 75.2 - - - +
314B SER* 1.3 58.8 + - - +
315B THR* 2.9 13.7 + - - -
316B GLU* 3.0 18.2 + - - +
318B PHE* 4.6 3.6 - - - -
323B TRP* 3.9 14.7 - - - -
340B ILE* 3.3 27.6 - - - +
341B PHE* 4.2 23.3 - - - -
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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