Contacts of the helix formed by residues 338 - 356 (chain A) in PDB entry 1IEX
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 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A LEU* 4.4 13.2 - - + -
335A GLY* 4.6 4.0 - - - +
336A VAL 4.1 5.2 - - - +
337A ILE* 1.3 94.6 - - + +
339A MET* 1.3 65.6 + - - +
340A SER* 3.8 19.3 - - - +
341A ARG* 3.2 25.5 + - + +
342A ILE* 3.6 5.3 + - - +
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Residues in contact with MET 339 (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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25A LEU* 4.0 27.4 - - + -
28A LYS* 3.1 24.2 - - + +
332A VAL* 4.1 15.5 - - + +
337A ILE 3.8 1.0 + - - -
338A PRO* 1.3 73.3 - - - +
340A SER* 1.3 56.4 + - - +
342A ILE* 3.2 10.7 + - + +
343A ASP* 2.8 63.2 + - - +
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Residues in contact with SER 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A PRO* 3.8 16.5 - - - +
339A MET* 1.3 80.3 - - - +
341A ARG* 1.3 57.9 + - - +
343A ASP* 3.5 8.7 + - - +
344A ASP* 2.9 28.6 + - - +
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Residues in contact with ARG 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A MET* 6.0 0.2 - - - -
273A LYS* 3.4 4.2 - - - +
308A ILE* 3.0 44.9 + - + +
309A LEU* 4.8 14.4 - - + +
311A GLY* 3.8 10.2 - - - -
312A LEU 2.9 22.6 + - - -
313A ASP* 2.9 21.4 + - - -
337A ILE* 4.3 6.1 - - + -
338A PRO* 3.2 22.8 + - + +
339A MET 3.2 0.2 - - - -
340A SER* 1.3 77.9 + - - +
342A ILE* 1.3 67.1 + - - +
344A ASP* 2.7 31.6 + - - +
345A ALA* 3.1 26.6 + - - +
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Residues in contact with ILE 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.7 6.3 - - + -
28A LYS* 4.0 33.9 - - + -
29A ILE* 5.0 3.1 - - + -
32A MET* 4.1 27.8 - - + -
308A ILE* 4.8 3.1 - - + -
328A LEU* 4.4 15.7 - - + -
332A VAL* 4.1 28.5 - - + -
337A ILE* 4.4 7.9 - - + -
338A PRO 3.8 13.0 - - - +
339A MET* 3.2 18.3 + - + +
341A ARG* 1.3 78.3 - - - +
343A ASP* 1.3 63.6 + - - +
345A ALA* 3.1 7.2 + - - +
346A VAL* 3.0 22.9 + - + +
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Residues in contact with ASP 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.2 24.2 - - + +
28A LYS* 2.7 35.2 + - - +
339A MET* 2.8 30.1 + - - +
340A SER* 3.7 9.1 - - - +
342A ILE* 1.3 76.4 - - - +
344A ASP* 1.3 54.1 + - - +
346A VAL* 3.6 1.3 + - - +
347A THR* 2.7 39.3 + - - +
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Residues in contact with ASP 344 (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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273A LYS* 3.5 6.4 + - - +
340A SER 2.9 15.8 + - - +
341A ARG* 2.7 37.1 + - - +
342A ILE 3.2 0.2 - - - -
343A ASP* 1.3 77.2 - - - +
345A ALA* 1.3 61.4 + - - +
347A THR* 3.3 7.2 + - - +
348A ARG* 3.1 53.8 + - - +
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Residues in contact with ALA 345 (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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32A MET* 3.7 28.0 - - + -
313A ASP* 3.6 34.2 - - - +
341A ARG* 3.1 16.6 + - - +
342A ILE 3.5 7.9 - - - +
344A ASP* 1.3 76.3 - - - +
346A VAL* 1.3 61.7 + - - +
348A ARG* 3.3 4.9 + - - +
349A ILE* 3.1 28.5 + - - +
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Residues in contact with VAL 346 (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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20A LEU* 3.6 25.4 - - + -
23A MET* 4.0 17.0 - - + -
28A LYS* 3.5 39.9 - - + +
31A GLN* 4.5 7.2 - - + -
32A MET* 4.2 9.6 - - + -
342A ILE* 3.0 17.0 + - + +
343A ASP* 4.1 0.4 - - - +
345A ALA* 1.3 71.1 - - - +
347A THR* 1.3 61.9 + - - +
349A ILE* 3.9 6.6 - - - +
350A LEU* 3.0 44.8 + - + +
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Residues in contact with THR 347 (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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13A GLU* 5.2 0.4 - - - +
16A VAL* 3.9 24.6 - - + +
20A LEU* 3.6 20.1 - - - +
343A ASP 2.7 25.1 + - - -
344A ASP* 3.5 9.1 - - - +
345A ALA 3.2 0.2 - - - -
346A VAL* 1.3 76.8 - - - +
348A ARG* 1.3 58.4 + - + +
350A LEU* 3.8 0.7 - - - -
351A ARG* 2.9 55.5 + - - +
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Residues in contact with ARG 348 (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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273A LYS* 3.7 33.1 + - - +
278A PHE* 2.9 30.9 + - - -
279A LYS* 3.6 21.6 - - - +
280A GLY 2.9 30.0 + - - +
281A PHE* 3.8 9.1 + - + +
313A ASP* 3.4 19.5 - - - +
344A ASP* 3.1 42.2 + - - +
345A ALA 3.3 6.0 + - - +
347A THR* 1.3 77.1 - - + +
349A ILE* 1.3 63.8 + - - +
351A ARG* 3.4 21.2 + - - +
352A VAL* 3.3 27.9 + - - +
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Residues in contact with ILE 349 (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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31A GLN* 3.3 47.1 - - + +
32A MET* 4.0 6.1 - - + +
281A PHE* 3.7 27.5 - - + -
313A ASP* 3.6 25.6 - - + +
314A MET* 3.9 24.2 - - + -
345A ALA 3.1 17.3 + - - +
346A VAL* 3.4 6.3 + - - +
348A ARG* 1.3 76.1 - - - +
350A LEU* 1.3 62.5 + - + +
352A VAL* 3.5 3.8 + - - +
353A LYS* 3.3 31.2 + - - +
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Residues in contact with LEU 350 (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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16A VAL* 4.1 17.9 - - + +
19A LEU* 3.8 41.3 - - + -
20A LEU* 4.6 7.2 - - + +
23A MET* 4.1 6.7 - - - -
31A GLN* 4.1 20.2 - - + +
88A ILE* 4.2 15.3 - - + -
346A VAL* 3.0 39.4 + - + +
347A THR 3.9 2.2 - - - +
349A ILE* 1.3 74.8 - - + +
351A ARG* 1.3 66.5 + - - +
353A LYS* 3.2 6.0 + - + +
354A PHE* 2.9 33.4 + - + -
359A PHE* 4.5 7.0 - - + -
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Residues in contact with ARG 351 (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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12A VAL* 4.1 5.1 - - + +
13A GLU* 2.7 41.7 + - - +
16A VAL* 3.8 13.6 - - + +
192A MET* 4.2 12.1 - - + +
193A PRO* 3.9 21.5 - - + -
279A LYS* 3.0 46.8 + - - +
347A THR* 2.9 39.6 + - - +
348A ARG* 3.6 23.1 - - - +
349A ILE 3.3 0.2 - - - -
350A LEU* 1.3 76.1 - - - +
352A VAL* 1.3 55.4 + - - +
354A PHE* 4.0 1.2 - - - +
355A THR* 2.7 42.0 + - - +
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Residues in contact with VAL 352 (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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91A ILE* 4.9 2.0 - - + -
193A PRO* 4.0 17.9 - - + -
195A VAL* 5.6 0.6 - - + +
202A ALA* 4.8 1.6 - - + -
247A SER* 3.7 31.9 - - - +
248A THR* 4.9 0.4 - - + -
280A GLY* 4.1 5.2 - - - -
281A PHE* 3.6 28.5 - - + -
348A ARG 3.3 13.6 + - - +
349A ILE 3.8 7.4 - - - +
350A LEU 3.2 0.4 - - - -
351A ARG* 1.3 78.7 - - + +
353A LYS* 1.3 62.4 + - + +
355A THR* 3.4 4.9 + - - -
356A MET* 3.0 50.4 + - + +
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Residues in contact with LYS 353 (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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31A GLN* 3.0 28.6 + - - +
51A GLY* 2.9 27.1 + - - -
88A ILE* 4.2 6.3 - - + +
89A PRO 2.8 29.0 + - - +
91A ILE* 4.2 23.6 - - + -
281A PHE* 5.9 1.3 - - + -
314A MET* 5.5 0.2 - - - -
349A ILE* 3.3 23.7 + - + +
350A LEU* 3.2 11.3 + - + +
352A VAL* 1.3 77.9 - - + +
354A PHE* 1.3 63.5 + - - +
356A MET* 3.4 10.8 - - - +
358A LEU* 3.1 42.8 + - + +
359A PHE* 4.0 14.3 - - + -
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Residues in contact with PHE 354 (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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5A TYR* 3.6 13.5 - - + -
12A VAL* 4.2 21.3 - - + +
15A ARG* 3.5 71.6 + - + +
16A VAL* 3.6 21.5 - - + -
19A LEU* 3.9 21.5 - - + -
350A LEU* 2.9 27.7 + - + +
351A ARG 4.0 2.9 - - - +
353A LYS* 1.3 76.0 - - - +
355A THR* 1.3 62.1 + - - +
357A GLY* 3.2 13.5 + - - -
358A LEU 5.1 0.2 - - - +
359A PHE* 3.4 40.6 - + - +
360A GLU* 4.8 1.2 - - - +
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Residues in contact with THR 355 (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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12A VAL* 3.8 23.4 - - + +
192A MET* 6.1 0.7 - - - +
193A PRO* 3.9 24.5 + - - +
194A PHE* 4.3 16.6 - - + -
195A VAL* 3.7 14.4 - - + +
196A ALA 5.6 0.2 - - - +
351A ARG* 2.7 28.4 + - - +
352A VAL* 3.8 5.6 - - - -
354A PHE* 1.3 78.3 - - - +
356A MET* 1.3 59.5 + - - +
357A GLY 3.1 1.4 + - - -
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Residues in contact with MET 356 (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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91A ILE* 3.6 23.1 - - + -
136A ARG* 4.9 9.2 + - - +
141A GLN* 4.8 12.1 - - - +
195A VAL* 3.6 33.9 - - + -
196A ALA 6.0 0.2 - - - -
197A GLY* 4.5 19.5 - - - +
198A LYS* 5.6 0.3 - - - -
202A ALA* 3.5 26.0 - - + -
352A VAL* 3.0 45.2 + - + +
353A LYS* 3.4 11.4 - - - +
355A THR* 1.3 75.9 - - - +
357A GLY* 1.3 60.2 + - - +
358A LEU* 4.1 20.6 - - + +
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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
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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