Contacts of the helix formed by residues 262 - 279 (chain M) in PDB entry 5LN3
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 GLY 262 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201L SER* 4.4 3.1 - - - +
204L VAL* 4.5 22.9 - - - -
260M PHE 3.6 2.8 + - - -
261M ILE* 1.4 71.3 - - - +
263M ASP* 1.4 61.3 + - - +
264M GLY 3.4 4.1 + - - -
265M ALA* 3.5 17.8 + - - +
266M LYS* 3.6 22.5 + - - +
305M GLU* 6.2 1.2 - - - +
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Residues in contact with ASP 263 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206L LYS* 4.1 11.5 + - - +
170M SER* 5.8 0.3 - - - -
173M LYS* 2.9 27.6 + - - -
258M GLN* 3.9 10.3 - - + +
260M PHE* 3.5 38.3 + - + +
261M ILE 3.4 2.2 + - - -
262M GLY* 1.4 74.1 - - - +
264M GLY* 1.4 63.4 + - - +
266M LYS* 3.2 19.2 + - - +
267M LEU* 3.1 33.3 + - - +
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Residues in contact with GLY 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256M LEU* 3.8 23.7 + - - +
258M GLN* 5.1 1.2 - - - +
260M PHE 5.4 0.2 + - - -
262M GLY 3.4 0.8 - - - -
263M ASP* 1.4 74.8 - - - +
265M ALA* 1.4 64.6 + - - +
267M LEU* 3.0 10.8 + - - +
268M VAL* 3.0 26.6 + - - +
309M THR* 4.5 15.3 - - - -
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Residues in contact with ALA 265 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201L SER* 3.4 29.6 - - - +
262M GLY* 3.5 11.5 + - - +
263M ASP 3.3 0.8 - - - -
264M GLY* 1.4 74.9 - - - +
266M LYS* 1.3 57.8 + - - +
268M VAL* 3.2 14.0 - - - +
269M ARG* 3.0 51.3 + - - +
308M ARG* 6.0 0.9 - - + -
309M THR* 4.8 6.8 + - - +
312M GLU* 3.9 9.2 - - + -
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Residues in contact with LYS 266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201L SER 5.0 2.4 + - - -
202L SER* 5.3 1.2 + - - +
204L VAL 4.0 7.7 + - - -
205L ASP* 3.4 27.2 + - - +
206L LYS* 3.4 31.0 - - - +
207L TYR* 6.4 0.4 - - - -
169M ASP* 5.5 6.7 - - - +
262M GLY 3.6 19.9 + - - +
263M ASP* 3.4 12.6 - - - +
264M GLY 3.2 0.2 - - - -
265M ALA* 1.3 75.1 - - - +
267M LEU* 1.4 60.7 + - + +
269M ARG* 3.3 23.8 + - - +
270M ASP* 3.0 31.8 + - - +
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Residues in contact with LEU 267 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170M SER* 4.3 26.0 - - - +
172M VAL* 3.7 33.0 - - + +
173M LYS* 5.0 10.5 - - + +
255M GLN 4.7 4.5 - - - +
256M LEU* 4.3 33.7 - - + +
258M GLN* 4.7 13.5 - - + +
263M ASP* 3.1 35.2 + - - +
264M GLY* 3.0 8.9 + - - +
266M LYS* 1.4 78.8 - - + +
268M VAL* 1.4 55.6 + - - +
270M ASP* 3.3 8.5 - - + +
271M ALA* 2.9 26.6 + - - +
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Residues in contact with VAL 268 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256M LEU* 3.9 33.9 - - + -
264M GLY 3.0 17.3 + - - +
265M ALA* 3.2 21.1 - - - +
267M LEU* 1.4 71.7 - - - +
269M ARG* 1.4 64.6 + - - +
271M ALA* 3.2 9.7 + - + +
272M PHE* 3.1 22.0 + - - +
291M ILE* 6.2 0.7 - - + -
309M THR* 4.5 11.9 - - + +
312M GLU* 3.8 20.6 - - + +
313M LEU* 5.2 14.8 - - + +
316M GLN* 3.9 12.0 + - - +
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Residues in contact with ARG 269 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199L VAL* 3.9 5.8 - - - +
201L SER* 3.5 17.4 + - - -
202L SER* 3.6 24.3 + - - +
265M ALA* 3.0 24.3 + - - +
266M LYS* 3.3 40.7 + - - +
268M VAL* 1.4 75.7 - - - +
270M ASP* 1.4 58.0 + - - +
272M PHE* 3.3 7.3 + - - +
273M ALA* 3.1 26.2 + - - +
312M GLU* 3.4 37.2 + - - +
316M GLN* 3.6 18.8 - - - +
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Residues in contact with ASP 270 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167M GLU* 3.5 36.0 - - - +
168M TYR 4.6 4.7 + - - +
170M SER 3.5 21.7 - - - +
171M ARG* 3.6 12.8 - - - -
172M VAL* 4.0 2.6 + - + -
266M LYS 3.0 17.1 + - - +
267M LEU* 3.3 9.4 - - + +
269M ARG* 1.4 74.3 - - - +
271M ALA* 1.3 58.5 + - - +
272M PHE 3.1 0.2 - - - -
273M ALA* 3.2 7.4 + - - +
274M LEU* 2.9 41.0 + - - +
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Residues in contact with ALA 271 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172M VAL* 4.7 4.0 - - + -
175M MET* 4.5 19.7 - - + +
249M LEU* 6.1 0.7 - - - +
251M LEU* 5.3 10.5 - - + -
267M LEU 2.9 13.9 + - - +
268M VAL* 3.3 16.6 - - + +
270M ASP* 1.3 76.0 - - - +
272M PHE* 1.4 57.7 + - - +
274M LEU* 3.6 12.5 + - - +
275M ALA* 3.1 26.9 + - - +
283M ILE* 4.7 11.3 - - + +
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Residues in contact with PHE 272 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221M LYS* 4.4 11.0 - - - -
268M VAL 3.1 6.5 + - - +
269M ARG 3.4 6.1 - - - +
271M ALA* 1.4 81.5 - - - +
273M ALA* 1.3 58.8 + - + +
275M ALA* 3.1 10.3 - - - +
276M LYS* 3.0 48.3 + - - +
283M ILE* 5.0 6.5 - - + -
316M GLN* 3.2 52.3 - - + +
317M LEU* 6.0 4.0 - - + -
320M PHE* 5.4 12.6 - + - -
323M ASN* 3.9 20.9 - - - -
326M VAL* 4.7 17.9 - - + +
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Residues in contact with ALA 273 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167M GLU* 3.6 18.8 - - + +
269M ARG 3.1 13.6 + - - +
270M ASP* 3.2 9.8 + - - +
272M PHE* 1.3 77.0 - - + +
274M LEU* 1.3 57.4 + - - +
276M LYS* 3.1 26.6 + - - +
277M GLU* 3.4 8.3 + - - +
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Residues in contact with LEU 274 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167M GLU* 3.2 26.0 - - - +
171M ARG* 4.5 23.1 - - + +
172M VAL* 4.6 5.2 - - + -
175M MET* 4.8 15.0 - - + -
270M ASP* 2.9 35.5 + - - +
271M ALA* 3.7 11.0 - - - +
273M ALA* 1.3 72.2 - - - +
275M ALA* 1.3 61.3 + - - +
277M GLU* 3.3 10.3 + - + +
278M LYS* 3.1 50.8 + - - +
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Residues in contact with ALA 275 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249M LEU* 5.5 3.4 - - + -
271M ALA 3.1 12.3 + - - +
272M PHE* 3.1 15.9 - - - +
274M LEU* 1.3 80.3 - - - +
276M LYS* 1.4 58.8 + - - +
278M LYS* 3.3 4.6 + - - +
279M ALA* 3.3 22.0 + - - +
281M SER* 4.0 22.3 + - - -
283M ILE* 4.3 17.5 - - + -
325M GLN 4.3 5.2 - - - +
326M VAL* 4.4 13.0 - - + -
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Residues in contact with LYS 276 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272M PHE* 3.0 43.7 + - - +
273M ALA* 3.1 14.7 + - - +
275M ALA* 1.4 77.4 - - - +
277M GLU* 1.3 60.8 + - - +
279M ALA* 3.9 6.1 + - - +
323M ASN* 4.4 11.1 - - - +
325M GLN* 3.1 52.5 + - - +
326M VAL* 5.4 2.3 - - - +
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Residues in contact with GLU 277 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273M ALA 3.4 6.8 + - - +
274M LEU* 3.3 11.5 + - + +
276M LYS* 1.3 81.2 - - - +
278M LYS* 1.4 82.5 + - - +
279M ALA* 3.5 1.0 + - - +
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Residues in contact with LYS 278 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175M MET* 6.3 1.6 - - - -
177M VAL* 5.1 14.4 - - - -
247M THR* 4.4 17.7 + - + +
249M LEU* 4.6 21.1 - - + -
274M LEU* 3.1 50.6 + - + +
275M ALA* 3.3 2.6 + - - +
277M GLU* 1.4 90.4 + - - +
279M ALA* 1.4 69.5 + - - +
280M PRO* 3.4 5.3 - - - +
281M SER* 3.7 20.0 - - - +
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Residues in contact with ALA 279 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275M ALA 3.3 8.3 + - - -
276M LYS 4.1 7.4 - - - +
277M GLU 3.3 2.7 - - - +
278M LYS* 1.4 82.0 - - - +
280M PRO* 1.3 70.3 + - + +
325M GLN* 4.1 32.3 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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