Contacts of the helix formed by residues 278 - 299 (chain A) in PDB entry 5NDD
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 SER 278 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LEU* 4.8 7.3 - - - +
276A GLU 3.6 2.2 - - - -
277A ASN* 1.3 77.2 - - - +
279A GLU* 1.3 63.5 + - - +
280A LYS 3.3 0.7 - - - -
281A LYS* 3.4 6.7 + - - +
282A ARG* 3.2 23.6 + - - +
2002A LEU* 4.5 17.8 + - - -
2003A GLU* 4.6 10.4 - - - +
2006A TRP* 4.2 17.8 - - - +
2045A PRO* 3.8 23.6 - - - -
2105A LEU* 3.5 18.7 + - - +
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLU 5.2 1.3 + - - +
277A ASN* 4.4 0.6 - - - +
278A SER* 1.3 82.1 + - - +
280A LYS* 1.3 67.0 + - - +
282A ARG* 3.2 22.8 + - - +
283A LYS* 3.4 33.8 + - - +
2003A GLU* 3.2 31.8 - - + +
2006A TRP* 6.0 4.7 - - + -
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Residues in contact with LYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ASN* 3.7 41.1 + - + +
278A SER 3.3 0.4 - - - -
279A GLU* 1.3 84.8 + - - +
281A LYS* 1.3 61.1 + - - +
283A LYS* 3.5 10.6 + - + +
284A ARG* 3.0 63.4 + - + +
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Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ARG* 3.1 31.2 - - - +
177A ILE* 4.6 5.5 - - - +
269A LEU* 3.8 32.0 - - + +
277A ASN 3.7 12.4 + - - +
278A SER* 3.4 10.8 + - - +
279A GLU 3.2 0.4 - - - -
280A LYS* 1.3 78.6 - - - +
282A ARG* 1.3 63.8 + - - +
284A ARG* 3.4 15.9 + - + +
285A ALA* 3.3 20.8 + - - +
349A HIS* 5.6 4.9 + - - -
2045A PRO* 4.1 23.9 + - + +
2048A GLU* 3.4 29.5 + - - +
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Residues in contact with ARG 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE* 5.5 4.5 - - + +
269A LEU* 4.2 29.1 - - + +
278A SER 3.2 13.6 + - - +
279A GLU* 3.2 28.8 + - - +
280A LYS 3.3 0.2 - - - -
281A LYS* 1.3 77.4 - - - +
283A LYS* 1.3 75.6 + - - +
285A ALA* 3.3 3.6 + - - +
286A ILE* 3.2 46.2 + - + +
2000A ALA* 4.6 9.0 - - + +
2003A GLU* 3.1 43.2 + - - -
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLU* 3.4 31.5 + - - +
280A LYS* 3.7 11.4 - - + +
281A LYS 3.3 0.6 - - - -
282A ARG* 1.3 93.2 - - - +
284A ARG* 1.3 63.2 + - + +
286A ILE* 3.5 8.4 + - + +
287A LYS* 3.1 53.5 + - - +
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A LYS* 3.0 53.9 + - + +
281A LYS* 3.7 15.2 - - + +
282A ARG 3.3 0.6 - - - -
283A LYS* 1.3 75.4 - - + +
285A ALA* 1.3 61.4 + - - +
287A LYS* 3.6 10.5 + - + +
288A LEU* 3.0 27.7 + - - +
346A PHE* 3.9 29.6 - - + +
349A HIS* 4.3 8.3 + - - -
352A ARG* 3.0 54.7 - - - +
356A LYS* 5.7 3.8 - - - +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ARG* 6.1 2.5 - - - +
262A TYR* 4.4 4.5 - - - -
265A MET* 4.2 15.9 - - - -
266A ILE* 4.6 11.8 - - + +
269A LEU* 3.7 28.7 - - + -
281A LYS 3.3 5.7 + - - +
282A ARG* 3.3 8.9 + - - +
284A ARG* 1.3 76.5 - - - +
286A ILE* 1.3 61.9 + - - +
288A LEU* 3.2 12.2 + - - +
289A ALA* 2.9 27.8 + - - +
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A ILE* 4.5 26.7 - - + -
282A ARG* 3.2 44.1 + - + +
283A LYS* 3.8 8.7 - - - +
285A ALA* 1.3 74.7 - - - +
287A LYS* 1.3 64.1 + - + +
289A ALA* 3.0 9.8 + - + +
290A VAL* 2.8 41.2 + - + +
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Residues in contact with LYS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A LYS* 3.1 44.2 + - - +
284A ARG* 3.9 8.0 - - + +
286A ILE* 1.3 78.4 - - + +
288A LEU* 1.3 53.1 + - - +
290A VAL* 3.3 9.3 + - - +
291A THR* 2.6 38.1 + - - -
346A PHE* 3.7 32.8 - - + -
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 5.8 1.6 - - + -
170A SER* 6.3 0.7 - - - -
173A ARG* 4.7 12.8 - - - +
262A TYR* 3.4 33.0 - - + +
265A MET* 5.0 3.8 - - + -
284A ARG 3.0 15.3 + - - +
285A ALA* 3.3 13.7 - - - +
287A LYS* 1.3 75.3 - - - +
289A ALA* 1.3 59.2 + - - +
291A THR* 3.3 2.8 + - - -
292A VAL* 2.9 38.4 + - + +
343A VAL* 4.0 37.7 - - + +
346A PHE* 3.8 15.7 - - + +
347A VAL* 3.8 25.8 - - + -
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR* 4.0 28.4 - - + -
266A ILE* 4.1 18.2 - - + -
285A ALA 2.9 13.4 + - - +
286A ILE* 3.3 8.7 - - + +
288A LEU* 1.3 75.7 - - - +
290A VAL* 1.3 62.1 + - + +
292A VAL* 4.1 1.8 - - - +
293A ALA* 3.1 25.1 + - - +
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ILE* 2.8 31.5 + - + +
287A LYS* 3.6 10.1 - - - +
288A LEU 3.2 0.2 - - - -
289A ALA* 1.3 77.2 - - + +
291A THR* 1.3 65.0 + - - +
293A ALA* 3.3 6.5 + - + +
294A ALA* 3.0 25.4 + - + +
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Residues in contact with THR 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LYS 2.6 25.8 + - - -
288A LEU* 3.4 8.3 - - - -
290A VAL* 1.3 77.8 - - - +
292A VAL* 1.3 61.4 + - - +
294A ALA* 3.4 5.9 + - - +
295A MET* 3.2 20.6 + - - +
339A ILE* 3.6 25.0 - - + +
342A PHE* 3.9 15.9 - - + +
343A VAL* 3.8 24.0 - - + +
346A PHE* 3.2 18.4 - - - -
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 4.2 21.5 - - + -
170A SER* 5.0 0.7 - - - +
258A THR* 4.1 17.0 - - + -
262A TYR* 3.4 28.0 - - + +
288A LEU* 2.9 29.1 + - + +
289A ALA* 4.1 3.6 - - - +
291A THR* 1.3 73.7 - - - +
293A ALA* 1.3 61.5 + - - +
295A MET* 3.0 9.7 + - - +
296A TYR* 2.9 51.8 + - + -
343A VAL* 4.8 5.4 - - + -
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ALA 3.1 20.4 + - - +
290A VAL* 3.3 7.2 + - + +
292A VAL* 1.3 77.9 - - - +
294A ALA* 1.3 57.5 + - - +
296A TYR* 3.2 8.1 + - - +
297A LEU* 2.8 30.7 + - - +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A VAL* 3.0 19.0 + - + +
291A THR* 3.7 6.7 - - - +
293A ALA* 1.3 77.3 - - - +
295A MET* 1.3 56.9 + - - +
297A LEU* 4.2 7.4 - - + -
298A ILE* 2.9 49.1 + - + +
339A ILE* 5.5 7.0 - - + -
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Residues in contact with MET 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A SER* 5.6 1.6 - - - -
166A LEU* 3.6 26.5 - - + -
291A THR 3.2 10.6 + - - +
292A VAL* 3.0 11.1 + - - +
294A ALA* 1.3 78.1 - - - +
296A TYR* 1.3 57.7 + - + +
299A CYS* 2.9 38.8 + - - +
300A PHE* 3.3 24.2 + - + -
336A ASN* 3.9 23.6 - - + +
339A ILE* 3.6 35.6 - - + +
340A ASP* 3.5 26.2 - - - +
343A VAL* 4.0 14.8 - - + -
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Residues in contact with TYR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ILE* 3.6 27.2 + - + +
166A LEU* 4.1 7.0 - - + +
251A PHE* 4.2 16.6 - + - -
254A PRO 4.0 2.1 + - - -
255A ALA* 3.6 32.5 - - + -
258A THR* 3.3 25.4 + - + +
292A VAL* 2.9 44.3 + - + +
293A ALA* 3.6 10.1 - - - +
295A MET* 1.3 77.6 - - - +
297A LEU* 1.3 58.4 + - - +
298A ILE 3.4 0.5 + - - -
300A PHE* 3.4 34.2 + + - -
301A THR* 2.8 40.0 + - - +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A ALA 2.8 18.2 + - - +
294A ALA* 3.7 6.5 - - - +
296A TYR* 1.3 77.1 - - - +
298A ILE* 1.3 72.8 + - + +
301A THR* 4.4 6.2 - - - -
302A PRO* 3.3 17.5 - - - +
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Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ALA* 2.9 27.6 + - + +
297A LEU* 1.3 97.3 - - + +
299A CYS* 1.3 67.6 + - - +
302A PRO* 3.2 19.8 - - - +
329A ALA 4.9 1.0 - - - +
332A LEU* 4.0 41.2 - - + +
333A SER* 4.6 0.3 + - - -
335A LEU* 4.3 13.9 - - + -
339A ILE* 6.0 7.9 - - + -
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Residues in contact with CYS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A MET* 4.3 1.2 - - - +
295A MET* 2.9 22.4 + - - +
298A ILE* 1.3 86.4 - - - +
300A PHE* 1.3 68.3 + - + +
302A PRO* 4.2 0.2 - - - -
303A SER* 2.9 23.4 + - - -
332A LEU 3.4 13.0 - - - -
333A SER* 3.2 27.8 - - - +
335A LEU* 3.9 7.9 - - - -
336A ASN* 3.3 39.3 - - + -
339A ILE* 5.0 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
------------------------------------------------------------
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