Contacts of the helix formed by residues 307 - 326 (chain P) in PDB entry 2IMW
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 307 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273P TYR* 3.1 5.7 + - - -
305P GLY 3.8 4.0 + - - -
306P ILE* 1.3 74.1 - - - +
308P LYS* 1.3 65.4 + - - +
309P GLU* 3.5 17.3 + - - +
310P THR* 3.1 28.2 + - - -
311P ALA 2.9 17.7 + - - -
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Residues in contact with LYS 308 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269P ILE* 4.1 2.2 - - + -
270P GLU* 3.1 39.7 + - - +
273P TYR* 3.6 54.5 + - + +
307P SER* 1.3 73.5 - - - +
309P GLU* 1.3 65.6 + - - +
311P ALA* 3.2 2.1 + - - +
312P TYR* 2.9 47.6 + - + -
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Residues in contact with GLU 309 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307P SER* 3.5 18.8 + - - +
308P LYS* 1.3 80.4 + - - +
310P THR* 1.3 64.4 - - - +
312P TYR* 3.2 9.6 + - - +
313P SER* 3.1 23.3 + - - -
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Residues in contact with THR 310 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302P PHE* 3.8 34.3 - - + -
304P HIS* 5.2 6.3 + - - +
305P GLY 5.9 0.2 - - - -
306P ILE* 4.0 13.0 - - + -
307P SER* 3.1 23.4 + - - -
309P GLU* 1.3 74.8 - - - +
311P ALA* 1.3 61.0 + - - +
313P SER* 3.3 7.7 + - - +
314P GLU* 2.8 31.8 + - + +
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Residues in contact with ALA 311 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269P ILE* 3.7 7.7 - - + +
273P TYR* 3.5 35.2 - - + +
284P ILE* 3.7 8.3 - - - +
306P ILE* 3.5 10.9 - - + +
307P SER 2.9 5.9 + - - -
308P LYS 3.2 10.1 + - - +
310P THR* 1.3 77.1 - - - +
312P TYR* 1.3 56.4 + - - +
314P GLU* 4.9 0.4 - - - -
315P SER* 3.0 33.6 + - - -
337P PHE* 4.0 14.6 - - + -
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Residues in contact with TYR 312 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266P PHE* 3.5 55.4 + + + +
269P ILE* 3.6 24.0 - - + -
270P GLU* 2.3 40.8 + - - +
308P LYS* 2.9 33.3 + - + +
309P GLU* 3.2 12.3 + - - +
311P ALA* 1.3 75.7 - - - +
313P SER* 1.3 60.3 + - - +
315P SER* 2.8 19.4 + - - -
316P VAL* 3.5 15.1 - - - +
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Residues in contact with SER 313 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309P GLU 3.1 16.5 + - - -
310P THR* 3.3 10.2 + - - +
312P TYR* 1.3 73.4 - - - +
314P GLU* 1.3 66.1 + - - +
316P VAL* 3.3 14.7 + - - +
317P LYS* 3.4 26.3 + - - +
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Residues in contact with GLU 314 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284P ILE* 4.1 10.1 - - + -
300P ARG* 3.3 44.9 + - + +
302P PHE* 3.8 24.6 - - + -
310P THR* 2.8 22.9 + - + +
311P ALA 4.3 1.3 - - - +
313P SER* 1.3 73.2 + - - +
315P SER* 1.3 56.8 + - - +
317P LYS* 3.2 28.3 + - - +
318P LEU* 2.9 50.9 + - + +
321P LYS* 5.7 0.5 + - - -
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Residues in contact with SER 315 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265P LEU* 3.6 21.0 - - - +
266P PHE* 4.0 1.4 - - - -
269P ILE* 3.3 19.8 - - - +
284P ILE* 4.2 8.9 - - - +
286P VAL* 3.4 24.4 - - - +
311P ALA 3.0 16.8 + - - -
312P TYR 2.8 21.3 + - - -
314P GLU* 1.3 77.7 - - - +
316P VAL* 1.3 56.3 + - - +
318P LEU* 4.5 0.4 - - - -
319P LEU* 2.9 27.9 + - - +
335P VAL* 4.9 0.7 - - - -
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Residues in contact with VAL 316 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258P LEU* 4.2 23.8 - - + -
262P LYS* 4.2 20.9 - - + -
265P LEU* 4.5 4.9 - - + -
266P PHE* 3.9 25.8 - - + -
312P TYR 3.5 15.5 - - - +
313P SER* 3.3 8.7 + - - +
314P GLU 3.2 0.4 - - - -
315P SER* 1.3 74.7 + - - +
317P LYS* 1.3 56.6 + - + +
319P LEU* 3.2 5.6 + - - +
320P GLN* 2.8 45.8 + - + +
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Residues in contact with LYS 317 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300P ARG* 5.2 5.7 - - - +
313P SER* 3.4 21.7 + - - +
314P GLU* 3.2 33.4 + - - +
316P VAL* 1.3 78.1 - - + +
318P LEU* 1.3 58.9 + - - +
320P GLN* 3.4 13.6 + - - +
321P LYS* 3.1 28.7 + - - +
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Residues in contact with LEU 318 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284P ILE* 3.7 24.9 - - + +
286P VAL* 3.7 25.6 - - + +
298P ARG* 3.6 28.1 - - + +
299P GLY* 3.6 25.8 - - - +
300P ARG* 4.1 1.1 - - + +
314P GLU* 2.9 45.0 + - + +
317P LYS* 1.3 73.7 - - - +
319P LEU* 1.3 66.0 + - - +
321P LYS* 3.1 26.1 + - - +
322P ILE* 3.0 23.9 + - - +
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Residues in contact with LEU 319 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258P LEU* 3.5 27.6 - - + +
261P ILE* 3.7 29.6 - - + -
262P LYS* 5.0 2.9 - - + +
265P LEU* 4.2 16.4 - - + -
286P VAL* 4.3 10.9 - - + +
315P SER 2.9 18.2 + - - +
316P VAL* 3.6 2.9 - - - +
318P LEU* 1.3 75.2 - - - +
320P GLN* 1.3 63.4 + - - +
322P ILE* 3.2 10.0 + - + +
323P LEU* 2.9 29.1 + - + +
330P ILE* 4.1 20.9 - - + -
333P ILE* 3.9 24.9 - - + -
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Residues in contact with GLN 320 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258P LEU* 3.5 34.7 - - + +
316P VAL* 2.8 29.2 + - + +
317P LYS* 3.5 13.1 - - - +
318P LEU 3.3 0.2 - - - -
319P LEU* 1.3 72.2 - - - +
321P LYS* 1.3 61.4 + - - +
323P LEU* 3.4 11.2 + - + +
324P GLU* 3.1 39.6 + - - +
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Residues in contact with LYS 321 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298P ARG* 3.8 27.1 - - + -
299P GLY 4.8 5.1 + - - -
300P ARG* 6.3 0.2 - - - +
314P GLU* 5.7 0.6 + - - -
317P LYS 3.1 13.7 + - - +
318P LEU* 3.1 28.9 + - - +
320P GLN* 1.3 74.5 - - - +
322P ILE* 1.3 63.5 + - - +
324P GLU* 3.4 11.7 + - - +
325P GLU* 3.1 48.9 + - - +
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Residues in contact with ILE 322 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286P VAL* 3.6 43.5 - - + +
288P ALA* 4.1 21.3 - - + -
290P THR* 6.6 0.4 - - + -
296P VAL* 3.9 34.5 - - + +
298P ARG* 3.4 26.0 - - + +
318P LEU 3.0 13.0 + - - +
319P LEU* 3.2 9.2 + - + +
321P LYS* 1.3 75.1 - - - +
323P LEU* 1.3 61.9 - - - +
325P GLU* 3.1 2.3 + - - -
326P ASP* 3.0 30.4 + - + +
330P ILE* 4.2 14.1 - - + -
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Residues in contact with LEU 323 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256P ARG* 2.8 70.4 + - - +
258P LEU* 4.2 21.5 - - + -
261P ILE* 4.5 2.9 - - + -
319P LEU* 2.9 34.1 + - + +
320P GLN* 3.5 11.0 - - + +
322P ILE* 1.3 76.5 - - - +
324P GLU* 1.3 59.5 + - + +
326P ASP 3.0 9.9 - - - +
330P ILE* 3.4 32.5 - - + -
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Residues in contact with GLU 324 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320P GLN* 3.1 33.9 + - - +
321P LYS* 3.7 10.8 - - - +
322P ILE 3.2 0.2 - - - -
323P LEU* 1.3 80.0 - - + +
325P GLU* 1.3 66.9 + - + +
326P ASP 3.4 1.3 + - - -
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Residues in contact with GLU 325 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298P ARG* 2.8 42.7 + - - +
321P LYS* 3.1 34.1 + - - +
322P ILE 3.1 4.3 + - - +
324P GLU* 1.3 84.0 - - + +
326P ASP* 1.3 63.5 + - - +
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Residues in contact with ASP 326 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256P ARG* 2.7 25.8 + - - -
290P THR* 4.1 4.2 - - + +
296P VAL* 3.5 27.3 - - + +
298P ARG* 5.9 0.2 + - - -
322P ILE* 3.0 15.5 + - + +
323P LEU* 3.0 10.9 - - - +
324P GLU 3.4 2.1 + - - -
325P GLU* 1.3 81.8 - - - +
327P GLU* 1.3 54.6 + - - +
328P ARG* 2.9 56.5 + - - +
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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