Contacts of the helix formed by residues 276 - 298 (chain L) in PDB entry 4XLN
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 PRO 276 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ASN* 5.0 3.1 - - - +
34J TYR* 3.4 34.1 - - + -
274L ARG* 3.4 24.0 - - - +
275L ILE* 1.3 97.4 - - + +
277L VAL* 1.3 65.9 + - - +
278L HIS* 3.5 23.8 - - + +
279L MET* 3.3 7.0 + - + +
280L VAL* 3.2 9.4 - - - +
20R T 4.1 12.3 - - + +
21R G 3.2 21.5 - - - +
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Residues in contact with VAL 277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264L ARG* 4.1 17.7 - - - +
267L ALA* 4.1 16.8 - - + +
268L ASP* 5.4 1.8 - - - +
275L ILE 3.9 0.4 + - - -
276L PRO* 1.3 69.9 - - + +
278L HIS* 1.3 66.3 + - + +
280L VAL* 2.8 29.8 + - - +
281L GLU* 2.9 21.9 + - + +
21R G 3.3 38.1 + - + +
22R T 3.5 27.4 - - + +
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Residues in contact with HIS 278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 3.7 5.5 + - - -
276L PRO* 3.5 25.0 - - + +
277L VAL* 1.3 80.1 + - + +
279L MET* 1.3 73.9 + - + +
281L GLU* 3.2 13.5 + - - +
282L THR* 2.9 37.3 + - + +
19R T 3.9 5.9 - - + +
20R T 2.9 78.2 + + + +
21R G 5.7 2.2 - - - +
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Residues in contact with MET 279 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 3.5 34.8 - - + +
275L ILE* 3.5 12.8 - - + -
276L PRO 3.3 11.0 + - - +
277L VAL 3.2 0.4 - - - -
278L HIS* 1.3 90.6 - - + +
280L VAL* 1.3 65.6 + - - +
282L THR* 2.7 25.1 + - - -
283L ILE* 2.9 43.1 + - + +
322L THR* 4.4 17.7 - - + +
325L ILE* 3.9 38.8 - - + -
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Residues in contact with VAL 280 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266L ILE* 5.4 9.9 - - + -
267L ALA* 4.2 23.6 - - + +
271L ARG* 3.9 18.2 - - - +
275L ILE* 3.5 21.5 - - + +
276L PRO 3.2 19.1 - - - +
277L VAL* 2.8 12.7 + - - +
279L MET* 1.3 72.9 - - - +
281L GLU* 1.3 59.1 + - + +
283L ILE* 3.3 10.4 + - + +
284L ASN* 2.9 50.6 + - - +
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Residues in contact with GLU 281 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L VAL* 2.9 26.6 + - + +
278L HIS* 3.3 12.5 + - - +
280L VAL* 1.3 75.6 - - + +
282L THR* 1.3 64.9 + - + +
284L ASN* 2.9 24.5 + - - +
285L LYS* 2.9 14.0 + - - +
22R T 5.5 0.2 - - - +
24S A 5.3 0.2 - - - +
25S G 3.4 40.0 + - - +
26S C 3.0 35.2 + - - -
27S A 4.6 4.5 + - - -
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Residues in contact with THR 282 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278L HIS* 2.9 21.6 + - + +
279L MET* 2.7 33.1 + - - -
281L GLU* 1.3 74.0 - - + +
283L ILE* 1.3 62.0 + - - +
285L LYS* 3.2 11.4 + - + +
286L LEU* 2.9 28.8 + - - +
314L TRP* 4.4 26.7 - - + -
318L ARG* 4.6 9.6 - - - +
322L THR* 4.9 5.0 - - - +
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Residues in contact with ILE 283 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271L ARG* 4.6 21.1 - - - +
275L ILE* 5.0 4.0 - - + -
279L MET* 2.9 44.1 + - + +
280L VAL* 3.4 12.6 - - + +
282L THR* 1.3 76.9 + - - +
284L ASN* 1.3 69.3 + - - +
286L LEU* 3.1 11.7 + - + +
287L SER* 2.9 26.7 + - - -
322L THR* 4.5 14.1 - - - +
325L ILE 5.4 0.4 - - - -
326L ALA* 4.3 28.5 - - + -
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Residues in contact with ASN 284 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263L ASN* 5.5 6.5 - - - +
266L ILE* 6.2 1.2 - - - +
280L VAL* 2.9 47.2 + - - +
281L GLU* 2.9 11.8 + - - +
283L ILE* 1.3 80.5 - - - +
285L LYS* 1.3 57.4 + - - +
287L SER* 3.4 5.1 + - - -
288L ARG* 2.9 32.3 + - - +
24S A 3.7 26.2 + - - +
25S G 3.6 19.3 + - - +
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Residues in contact with LYS 285 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281L GLU 2.9 11.4 + - - +
282L THR* 3.5 13.0 - - + +
284L ASN* 1.3 76.0 - - - +
286L LEU* 1.3 53.6 + - - +
288L ARG* 3.2 10.9 - - - +
289L THR* 2.7 39.6 + - - +
310L MET* 3.8 32.3 + - + +
314L TRP* 6.2 0.2 - - + -
25S G 4.5 16.5 + - - +
26S C 4.6 18.8 - - - +
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Residues in contact with LEU 286 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282L THR 2.9 19.4 + - - +
283L ILE* 3.3 14.6 - - + +
285L LYS* 1.3 76.5 - - - +
287L SER* 1.3 57.6 + - - +
289L THR* 3.2 8.1 + - - -
290L ALA* 2.9 27.3 + - - +
306L ILE* 4.2 7.8 - - + +
310L MET* 3.6 23.1 - - + -
314L TRP* 3.6 29.8 - - + -
319L VAL* 3.7 24.9 - - + +
322L THR* 3.1 32.5 - - - +
323L LEU* 5.2 3.4 - - + +
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Residues in contact with SER 287 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376I ARG* 3.6 21.7 + - - +
283L ILE* 2.9 19.4 + - - -
284L ASN* 4.0 5.6 - - - -
286L LEU* 1.3 75.7 - - - +
288L ARG* 1.3 57.0 + - - +
290L ALA* 3.3 8.3 - - - +
291L ARG* 2.9 41.6 + - - -
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Residues in contact with ARG 288 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284L ASN 2.9 19.1 + - - +
285L LYS* 3.2 11.4 - - - +
287L SER* 1.3 73.4 - - - +
289L THR* 1.3 67.3 + - - +
291L ARG* 3.1 11.8 + - - +
292L GLN* 3.0 26.2 + - + +
24S A 4.6 9.9 + - - -
25S G 3.5 28.7 + - - -
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Residues in contact with THR 289 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285L LYS* 2.7 21.4 + - - +
286L LEU 3.5 6.7 - - - -
288L ARG* 1.3 76.7 - - - +
290L ALA* 1.3 63.0 + - - +
292L GLN* 3.0 12.9 + - + +
293L LEU* 2.9 30.6 + - + +
306L ILE* 3.6 21.1 - - + +
309L ALA* 3.7 34.2 + - + +
310L MET* 3.5 16.6 - - - -
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Residues in contact with ALA 290 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376I ARG* 4.9 9.0 - - - +
286L LEU 2.9 12.6 + - - +
287L SER* 3.3 14.4 - - - +
289L THR* 1.3 76.8 - - - +
291L ARG* 1.3 63.5 + - - +
293L LEU* 3.3 11.4 - - - +
294L GLN* 2.9 31.1 + - - +
301L PRO* 4.6 9.4 - - + -
306L ILE* 3.5 9.8 - - + +
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Residues in contact with ARG 291 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358I ARG* 3.9 11.5 - - - +
374I ASN* 3.3 42.0 - - - +
375I SER* 5.1 7.8 + - - +
376I ARG* 3.3 44.1 - - - +
287L SER* 2.9 27.3 + - - -
288L ARG* 3.1 11.0 + - - +
290L ALA* 1.3 75.5 - - - +
292L GLN* 1.3 61.2 + - - +
294L GLN* 4.3 3.4 - - - +
295L GLN* 3.2 23.4 + - - +
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Residues in contact with GLN 292 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371I LYS* 6.0 4.6 - - - +
288L ARG* 3.0 15.9 + - + +
289L THR* 3.5 15.2 - - + +
291L ARG* 1.3 74.4 - - - +
293L LEU* 1.3 60.6 + - - +
294L GLN 3.1 1.3 - - - -
295L GLN* 3.0 11.1 + - + +
296L GLU* 3.0 44.6 + - + +
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Residues in contact with LEU 293 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289L THR* 2.9 30.0 + - + +
290L ALA* 3.3 15.5 - - - +
292L GLN* 1.3 73.2 - - - +
294L GLN* 1.3 56.7 + - - +
296L GLU* 3.7 14.3 + - + +
297L LEU* 2.9 35.3 + - + +
299L ARG 3.9 1.0 - - - +
301L PRO* 3.5 36.6 - - + -
305L GLU* 4.1 16.8 - - + +
306L ILE* 3.6 15.9 - - + -
309L ALA* 4.1 23.1 - - + -
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Residues in contact with GLN 294 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I PHE* 3.3 26.9 - - - -
117I HIS* 5.8 0.8 + - - -
375I SER* 3.0 29.9 + - - -
376I ARG* 6.2 0.8 - - - +
379I GLU* 3.4 21.6 + - - -
290L ALA 2.9 20.9 + - - +
291L ARG* 4.3 3.4 - - - +
293L LEU* 1.3 76.1 - - - +
295L GLN* 1.3 65.8 + - - +
296L GLU 3.2 0.2 - - - -
298L GLY 3.3 15.6 + - - -
299L ARG* 3.3 29.3 + - - +
300L GLU* 3.6 24.6 + - + +
301L PRO* 4.6 2.7 - - + -
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Residues in contact with GLN 295 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I GLU 5.1 0.6 + - - -
113I VAL* 3.4 30.5 - - - +
114I PHE* 3.4 31.3 + - - +
370I ALA* 3.3 33.0 + - + +
373I VAL* 3.2 27.5 - - - +
374I ASN* 5.1 0.5 - - - -
375I SER* 5.3 2.7 - - - +
291L ARG 3.2 14.8 + - - +
292L GLN* 3.0 12.5 + - + +
294L GLN* 1.3 84.2 + - - +
296L GLU* 1.3 66.4 + - + +
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Residues in contact with GLU 296 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I PHE* 5.5 0.5 - - - +
370I ALA* 6.5 0.7 - - + -
292L GLN* 3.0 43.5 + - + +
293L LEU* 3.9 9.8 + - + +
294L GLN 3.2 0.2 - - - -
295L GLN* 1.3 82.7 - - + +
297L LEU* 1.3 66.2 + - - +
298L GLY* 3.0 4.2 + - - -
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Residues in contact with LEU 297 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I TYR* 4.9 4.2 + - - -
293L LEU* 2.9 24.6 + - + +
296L GLU* 1.3 74.1 - - - +
298L GLY* 1.3 59.1 + - - +
299L ARG* 3.5 65.1 + - + +
300L GLU 4.9 2.9 - - - +
301L PRO* 5.2 0.7 - - + -
305L GLU* 3.7 25.4 - - - +
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Residues in contact with GLY 298 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I PRO* 4.1 5.7 - - - +
95I TYR* 4.0 18.3 + - - -
114I PHE* 3.3 49.7 - - - -
117I HIS* 4.2 0.5 - - - -
294L GLN 3.3 4.4 + - - -
296L GLU 3.0 7.0 + - - -
297L LEU* 1.3 78.3 - - - +
299L ARG* 1.3 64.3 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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