Contacts of the helix formed by residues 299 - 316 (chain B) in PDB entry 1N1E
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 ALA 299 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ARG* 4.0 12.3 - - + +
275B ASN* 3.4 17.5 - - - +
278B VAL* 3.7 29.8 - - + -
292B GLN* 4.6 10.2 + - - +
297B ALA 3.5 4.0 + - - +
298B VAL* 1.3 76.6 - - - +
300B GLU* 1.3 64.8 + - - +
301B GLY 3.2 2.5 - - - -
302B VAL* 3.1 24.0 + - + +
303B ALA* 4.2 1.9 + - - +
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PRO* 3.3 5.3 - - - +
95B THR* 2.8 34.3 + - - -
96B GLN* 4.7 9.2 + - - +
125B LYS 3.2 19.8 - - - +
126B GLY* 5.0 0.2 - - - -
211B ASN* 3.6 17.3 - - + +
275B ASN* 3.5 5.2 + - - +
298B VAL* 3.8 20.8 + - + +
299B ALA* 1.3 68.5 - - - +
301B GLY* 1.3 64.1 + - - +
302B VAL 3.2 0.6 + - - -
303B ALA* 3.3 6.3 + - - +
304B THR* 2.9 30.6 + - - +
401B NDE 2.7 41.0 + - - +
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Residues in contact with GLY 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ASN* 3.7 26.2 - - - +
212B VAL* 3.8 4.8 - - - +
215B ILE* 3.6 8.6 - - - +
275B ASN* 2.8 23.0 + - - -
300B GLU* 1.3 72.7 - - - +
302B VAL* 1.3 60.8 + - - +
304B THR* 4.0 6.3 - - - -
305B ALA* 3.1 25.1 + - - +
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 6.3 0.2 - - - +
215B ILE* 3.6 9.6 - - + +
278B VAL* 3.9 28.5 - - + -
288B ILE* 4.2 13.0 - - + -
292B GLN* 3.7 31.0 - - + +
299B ALA* 3.1 22.6 + - + +
301B GLY* 1.3 78.0 - - - +
303B ALA* 1.3 60.6 + - - +
305B ALA 3.6 1.0 + - - -
329B VAL* 3.8 19.0 - - + +
330B TYR* 3.0 28.6 - - + +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLN* 3.7 30.2 + - + +
129B ARG* 3.7 28.0 - - - +
299B ALA 4.2 1.9 + - - +
300B GLU* 3.3 9.1 + - - +
302B VAL* 1.3 80.0 - - + +
304B THR* 1.3 59.6 + - - +
307B PRO* 3.1 25.6 - - - +
330B TYR* 3.6 12.7 + - - -
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Residues in contact with THR 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLN* 4.7 1.9 + - - -
126B GLY* 3.5 9.2 - - - -
127B ILE* 3.2 45.4 + - + +
208B ALA 3.8 15.6 + - - +
212B VAL* 3.8 16.4 - - + -
300B GLU* 2.9 22.3 + - - +
301B GLY* 3.8 8.1 - - - -
303B ALA* 1.3 77.8 - - - +
305B ALA* 1.3 64.9 + - - +
307B PRO* 3.4 6.9 - - - +
308B LEU* 2.9 21.5 + - + +
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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
----------------------------------------------------------
212B VAL* 4.0 20.0 - - + -
301B GLY 3.1 17.1 + - - +
302B VAL 3.9 7.4 - - - +
303B ALA 3.4 1.2 - - - -
304B THR* 1.3 76.3 - - - +
306B ASP* 1.3 61.4 + - - +
308B LEU* 3.6 4.2 + - - +
309B MET* 3.2 18.0 + - - +
322B CYS 5.5 0.2 - - - +
326B TYR* 3.6 30.9 - - + +
329B VAL* 4.5 9.6 - - + -
330B TYR* 4.0 10.5 - - + -
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Residues in contact with ASP 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 5.8 2.1 - - - -
305B ALA* 1.3 76.4 - - - +
307B PRO* 1.3 72.1 - - + +
309B MET* 3.1 13.9 + - - +
310B ARG* 3.0 47.7 + - - +
326B TYR* 3.4 24.9 + - - -
330B TYR* 3.5 39.1 - - + +
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Residues in contact with PRO 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 3.7 25.3 - - + +
128B GLU 3.6 6.5 - - - +
129B ARG* 3.5 28.3 - - + +
132B LEU* 3.6 19.9 - - + +
303B ALA 3.1 27.4 - - - +
304B THR 3.4 7.6 - - - +
306B ASP* 1.3 93.5 - - + +
308B LEU* 1.3 54.1 + - - -
310B ARG* 3.4 11.6 + - - +
311B LEU* 2.9 30.5 + - - +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 4.0 20.8 - - + +
209B VAL* 4.0 19.1 - - + -
212B VAL* 3.9 22.2 - - + -
244B LEU* 3.6 31.4 - - + -
304B THR* 2.9 21.4 + - + +
305B ALA 3.7 5.2 - - - +
307B PRO* 1.3 74.5 - - - +
309B MET* 1.3 65.2 + - - +
311B LEU* 3.2 4.3 + - + +
312B ALA* 3.0 21.0 + - - +
319B MET* 4.0 10.5 - - + -
322B CYS* 3.9 33.9 - - + -
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Residues in contact with MET 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ALA 3.2 10.9 + - - +
306B ASP* 3.1 9.0 + - - +
308B LEU* 1.3 79.6 - - - +
310B ARG* 1.3 73.3 + - - +
312B ALA* 3.3 5.9 + - - +
313B LYS* 2.9 45.4 + - + +
322B CYS 6.0 0.2 - - - +
323B HIS* 4.5 21.5 - - + +
326B TYR* 3.8 51.4 - - + +
327B GLU* 5.6 0.2 - - - +
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 2.5 36.9 + - - +
130B SER* 4.0 13.7 + - - +
132B LEU* 3.9 25.3 - - + +
306B ASP* 3.0 44.0 + - - +
307B PRO* 3.8 15.5 - - - +
309B MET* 1.3 87.0 - - - +
311B LEU* 1.3 62.7 + - - +
313B LYS* 3.5 7.2 + - + +
314B GLN* 3.0 26.5 + - - +
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 4.3 11.7 - - + -
132B LEU* 4.0 32.0 - - + +
134B PHE* 4.1 27.8 - - + -
244B LEU* 4.7 7.9 - - + -
248B LEU* 4.2 16.8 - - + -
307B PRO 2.9 17.6 + - - +
308B LEU* 3.2 5.4 + - + +
310B ARG* 1.3 77.3 - - - +
312B ALA* 1.3 61.7 + - - +
314B GLN* 3.3 20.0 - - - +
315B LEU* 3.1 42.9 + - + +
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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
----------------------------------------------------------
244B LEU* 4.7 6.3 - - + +
308B LEU* 3.0 16.0 + - + +
309B MET* 3.8 6.5 - - - +
311B LEU* 1.3 73.9 - - - +
313B LYS* 1.3 55.1 + - - +
315B LEU* 3.2 1.1 + - - +
316B LYS 2.8 30.3 + - - -
317B VAL* 2.9 38.1 + - + +
319B MET* 3.7 24.9 - - + -
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Residues in contact with LYS 313 (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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309B MET* 2.9 33.9 + - + +
310B ARG* 3.7 7.4 - - + +
312B ALA* 1.3 75.8 - - - +
314B GLN* 1.3 63.6 + - - +
316B LYS* 3.1 18.2 + - - +
317B VAL 5.4 0.2 - - - -
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Residues in contact with GLN 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.8 27.7 - - - +
310B ARG* 3.0 12.6 + - - +
311B LEU* 3.3 20.0 - - + +
313B LYS* 1.3 77.7 - - - +
315B LEU* 1.3 64.6 + - + +
316B LYS* 3.7 6.9 + - - +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 3.7 25.1 - - + -
247B ALA* 4.0 24.6 - - + +
248B LEU* 3.8 27.4 - - + -
311B LEU* 3.1 30.6 + - + +
312B ALA 3.2 0.6 + - - +
314B GLN* 1.3 79.9 - - + +
316B LYS* 1.3 72.0 + - - +
317B VAL* 3.3 16.4 + - + +
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Residues in contact with LYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ALA 2.8 7.8 + - - -
313B LYS* 3.1 12.8 + - - +
314B GLN 4.4 5.7 + - - +
315B LEU* 1.3 81.6 - - - +
317B VAL* 1.3 58.0 - - - +
318B LYS* 3.9 11.0 + - - +
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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