Contacts of the helix formed by residues 360 - 376 (chain A) in PDB entry 3PMM
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 MSE 360 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 4.5 2.2 - - - -
58A LYS* 3.3 26.0 - - + +
336A LEU 5.4 0.2 + - - -
339A THR* 4.2 6.7 - - + +
340A SER 4.0 4.9 - - - +
341A PHE* 3.6 34.3 - - + -
342A GLY* 3.8 6.3 - - - +
358A THR* 3.3 17.6 + - + +
359A SER* 1.3 90.0 + - - +
361A PRO* 1.3 77.8 - - + +
362A TYR* 3.5 53.6 - - + +
363A GLY* 3.0 12.1 + - - -
364A GLN* 3.4 19.0 + - - +
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Residues in contact with PRO 361 (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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35A LEU* 3.5 7.1 - - + +
38A ILE* 3.6 27.4 - - + -
57A THR 5.0 1.6 - - - +
58A LYS* 4.1 22.4 - - + +
66A THR* 4.0 9.4 - - + +
360A MSE 1.3 93.2 - - + +
362A TYR* 1.3 58.6 + - + +
364A GLN 3.3 2.1 + - - +
365A ALA* 2.9 27.5 + - - +
380A IMD 3.4 47.6 - - + +
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Residues in contact with TYR 362 (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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65A TRP* 3.4 46.4 - + + -
66A THR* 3.9 12.3 - - + +
69A VAL* 5.8 1.1 - - + -
230A ARG* 3.2 38.5 + - - -
293A SER* 4.1 5.2 - - - -
339A THR* 3.9 4.5 - - + -
340A SER 2.6 25.3 + - - -
341A PHE* 2.9 23.6 + - - -
342A GLY* 3.1 5.9 + - - -
360A MSE 3.5 32.2 - - + +
361A PRO* 1.3 78.3 - - + +
363A GLY* 1.3 70.0 + - - +
365A ALA* 4.0 8.3 - - + -
366A MSE 2.8 44.0 + - + +
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Residues in contact with GLY 363 (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 SER* 4.0 11.9 - - - -
336A LEU* 3.4 27.3 - - - +
339A THR* 4.3 8.5 - - - -
360A MSE 3.0 9.7 + - - -
362A TYR* 1.3 85.0 - - - +
364A GLN* 1.3 68.7 + - - +
366A MSE 4.0 0.5 - - - +
367A ALA* 3.1 18.9 + - - +
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Residues in contact with GLN 364 (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 VAL* 3.3 18.2 - - + +
34A ASN* 2.9 26.7 - - + +
35A LEU* 4.1 17.9 - - + +
38A ILE* 3.8 7.3 - - - +
334A GLY 3.4 19.7 - - - +
335A GLU* 3.8 3.7 - - - +
336A LEU* 2.9 34.5 + - - +
359A SER* 3.3 20.5 + - - -
360A MSE 3.6 12.4 + - - +
361A PRO* 3.3 7.0 + - + +
363A GLY* 1.3 77.1 - - - +
365A ALA* 1.3 62.5 + - - +
367A ALA* 3.3 2.8 + - - -
368A ILE* 3.0 28.7 + - - +
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Residues in contact with ALA 365 (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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35A LEU* 4.4 3.7 - - + +
66A THR 4.5 3.6 - - - +
69A VAL* 3.9 13.2 - - + +
70A GLY* 3.6 32.5 - - - +
73A GLY* 5.0 0.5 - - - -
361A PRO 2.9 17.5 + - - +
362A TYR* 3.8 7.6 - - - +
363A GLY 3.3 0.2 - - - -
364A GLN* 1.3 76.7 - - - +
366A MSE 1.3 62.4 + - - +
368A ILE* 3.3 15.6 + - - +
369A LEU* 3.1 24.9 + - - +
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Residues in contact with MSE 366 (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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69A VAL* 4.4 9.9 - - + -
230A ARG* 4.1 9.6 - - + -
233A SER* 3.3 25.6 - - - +
234A TRP* 3.5 42.4 - - + -
237A MSE 4.9 4.7 - - - -
293A SER* 3.2 37.9 - - - +
296A ALA* 3.7 22.9 - - + +
297A GLY* 4.0 12.3 - - - +
300A TYR* 5.5 0.2 - - - +
362A TYR* 2.8 25.1 + - + +
363A GLY 4.1 2.0 - - - +
365A ALA* 1.3 73.3 - - - +
367A ALA* 1.3 61.2 + - - +
369A LEU* 3.3 8.3 + - + +
370A CYS* 3.0 24.4 + - - +
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Residues in contact with ALA 367 (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 VAL* 4.3 8.3 - - + -
296A ALA* 4.0 2.8 - - - +
326A ILE* 4.6 4.7 - - + -
330A ILE* 4.3 23.6 - - + -
336A LEU* 4.5 12.3 - - + -
363A GLY 3.1 17.9 + - - +
364A GLN* 3.5 6.7 - - - +
365A ALA 3.3 0.2 - - - -
366A MSE 1.3 74.5 - - - +
368A ILE* 1.3 64.1 + - - +
370A CYS* 3.5 9.5 + - - -
371A LEU* 3.0 33.2 + - + +
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Residues in contact with ILE 368 (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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28A ILE* 4.3 17.7 - - + +
31A VAL* 3.7 15.7 - - + -
32A THR* 3.5 30.7 - - - +
35A LEU* 3.8 27.4 - - + -
70A GLY 5.1 1.3 - - - +
73A GLY* 3.6 30.7 - - - +
74A ILE* 3.9 8.5 - - + +
86A MSE 5.1 0.9 - - + -
364A GLN 3.0 20.5 + - - +
365A ALA* 3.5 8.7 - - - +
366A MSE 3.3 0.2 - - - -
367A ALA* 1.3 76.1 - - - +
369A LEU* 1.3 61.6 + - - +
371A LEU* 4.3 2.1 - - - +
372A THR* 2.8 36.7 + - - +
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Residues in contact with LEU 369 (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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69A VAL* 3.7 35.7 - - + +
72A TYR* 4.1 10.3 - - + -
73A GLY* 3.5 27.4 - - - +
76A GLN* 3.5 32.9 - - + +
237A MSE 4.3 20.9 - - + -
300A TYR* 3.4 29.3 - - + -
365A ALA 3.1 8.7 + - - +
366A MSE 3.6 9.6 - - - +
367A ALA 3.2 0.2 - - - -
368A ILE* 1.3 80.9 - - - +
370A CYS* 1.3 64.0 + - - +
372A THR* 3.4 3.3 + - - -
373A GLU 3.0 19.1 + - - -
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Residues in contact with CYS 370 (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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296A ALA* 3.1 41.5 - - - +
299A ALA* 3.9 5.6 - - + -
300A TYR* 3.6 19.5 - - - +
303A LEU* 3.7 6.6 - - - +
323A ILE* 3.8 15.2 - - + +
326A ILE* 4.1 14.6 - - - -
366A MSE 3.0 13.7 + - - +
367A ALA* 3.6 13.0 - - - -
369A LEU* 1.3 76.9 - - - +
371A LEU* 1.3 61.6 + - - +
373A GLU 3.4 0.9 + - - -
374A TYR* 2.9 27.5 + - - +
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Residues in contact with LEU 371 (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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24A LEU* 4.0 18.7 - - + +
27A LEU* 3.9 18.8 - - + -
28A ILE* 3.6 27.2 - - + +
31A VAL* 5.1 2.2 - - + -
323A ILE* 4.3 19.5 - - + -
326A ILE* 4.5 5.6 - - + -
327A VAL* 4.0 18.6 - - + -
330A ILE* 3.7 26.9 - - + -
367A ALA* 3.0 24.2 + - + +
368A ILE* 5.3 0.2 - - - -
370A CYS* 1.3 80.0 - - - +
372A THR* 1.3 61.4 + - - +
374A TYR* 3.2 6.0 + - + +
375A LEU* 3.0 29.5 + - - +
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Residues in contact with THR 372 (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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28A ILE* 3.7 11.5 - - - +
73A GLY 4.8 1.8 - - - -
76A GLN* 3.8 14.8 - - + +
77A TYR* 3.6 54.3 - - + +
80A GLN* 3.0 36.6 + - - +
368A ILE* 2.8 25.6 + - - +
369A LEU* 3.8 4.5 - - - -
371A LEU* 1.3 74.7 - - - +
373A GLU* 1.3 64.4 + - - +
375A LEU* 3.3 10.4 + - - +
376A ARG 3.7 0.2 + - - -
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Residues in contact with GLU 373 (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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76A GLN* 4.6 6.7 + - - +
80A GLN* 5.1 0.2 - - - +
300A TYR* 3.8 22.7 - - + +
303A LEU* 3.5 28.5 - - + +
304A LYS* 3.6 26.8 + - - +
307A ARG* 2.8 47.9 + - - +
369A LEU 3.0 16.7 + - - +
370A CYS* 3.8 4.3 - - - +
372A THR* 1.3 75.8 - - - +
374A TYR* 1.3 62.8 + - - +
376A ARG* 3.0 26.3 + - - +
377A LYS* 4.2 2.4 + - - +
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Residues in contact with TYR 374 (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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17A ARG* 5.7 2.6 - - - +
18A PHE* 3.4 21.1 + + - -
19A ILE* 4.4 2.5 - - + -
24A LEU* 3.7 19.7 - - + -
303A LEU* 3.8 14.1 - - + +
320A GLU* 2.6 39.0 + - - -
323A ILE* 3.7 39.9 - - + -
370A CYS 2.9 18.3 + - - +
371A LEU* 3.2 7.8 + - - +
373A GLU* 1.3 76.3 - - - +
375A LEU* 1.3 56.8 + - - +
377A LYS* 2.9 56.9 + - + +
378A TYR* 3.7 28.2 + + - -
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Residues in contact with LEU 375 (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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21A ARG* 3.7 30.5 - - + -
24A LEU* 3.5 27.7 - - + +
25A GLN* 3.9 17.3 - - + +
28A ILE* 3.5 27.6 - - + -
77A TYR* 3.8 20.0 - - + -
80A GLN* 3.3 22.7 - - - +
81A THR* 5.4 0.2 - - + -
371A LEU 3.0 9.1 + - - +
372A THR* 3.3 8.1 - - - +
373A GLU 3.2 0.2 - - - -
374A TYR* 1.3 75.4 - - - +
376A ARG* 1.3 61.7 + - - +
377A LYS 3.0 0.2 - - - -
378A TYR* 3.0 26.1 + - + +
379A PHE* 3.7 8.8 - - - -
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Residues in contact with ARG 376 (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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76A GLN 5.5 0.4 + - - -
79A GLN* 4.5 17.2 + - - +
80A GLN* 3.7 40.1 - - - +
307A ARG* 3.7 56.7 - - - +
372A THR 3.7 1.3 + - - +
373A GLU* 3.0 24.5 + - - +
375A LEU* 1.3 78.4 - - - +
377A LYS* 1.3 61.8 + - + +
378A TYR 3.2 1.0 + - - -
379A PHE* 3.5 30.6 + - - +
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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
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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