Contacts of the helix formed by residues 337 - 349 (chain 0) in PDB entry 1O1F
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 TYR 337 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180 LYS* 3.8 20.6 - - + -
260 ALA* 4.5 11.0 - - + -
270 PRO* 3.6 43.1 - - + -
300 VAL* 4.1 17.7 - - + +
3340 GLU* 2.8 9.7 + - + +
3360 LYS* 1.3 129.4 + - + +
3380 SER* 1.4 62.4 + - - -
3390 VAL* 3.3 3.8 - - - -
3400 TRP* 3.0 8.6 + - + -
3410 ILE* 2.9 38.9 + - + +
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Residues in contact with SER 338 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1400 LEU 3.8 0.3 - - - +
1410 SER* 3.2 28.0 + - - -
1440 ALA* 3.5 12.2 - - - +
2980 VAL* 5.9 1.3 - - - +
2990 MET 4.4 2.6 + - - -
3000 SER* 3.7 15.6 - - - -
3320 PRO* 5.2 6.1 - - - +
3340 GLU* 3.8 8.3 + - - -
3350 ARG* 3.3 24.1 + - - +
3370 TYR* 1.4 72.1 - - - +
3390 VAL* 1.3 54.7 - - - +
3410 ILE* 3.1 8.0 + - - +
3420 GLY* 2.8 31.2 + - - -
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Residues in contact with VAL 339 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110 ASP* 3.4 34.8 - - + +
1060 THR* 4.2 2.0 - - + -
1370 GLN* 4.0 25.1 - - + +
1400 LEU* 3.3 26.2 - - + +
1410 SER* 3.1 25.3 + - - +
1540 ASP* 4.2 17.5 - - - +
3000 SER* 4.5 3.6 - - - +
3350 ARG 6.1 0.2 - - - +
3370 TYR* 5.0 1.1 - - - -
3380 SER* 1.3 81.0 - - - +
3400 TRP* 1.3 62.2 + - - +
3430 GLY 3.2 14.4 + - - -
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Residues in contact with TRP 340 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90 VAL* 2.8 45.1 + - + +
110 ASP* 4.0 9.8 + - + +
180 LYS* 3.4 39.1 + - + -
190 ALA* 3.6 7.0 - - - +
200 GLY* 3.6 26.7 - - - -
210 PHE 3.5 23.1 - - - -
240 ASP* 3.8 18.2 - - + -
250 ASP 4.3 0.7 - - - -
260 ALA* 3.5 28.0 - - - -
270 PRO* 3.7 17.9 - - + -
1060 THR* 6.2 0.2 - - - -
3370 TYR* 3.0 18.1 + - + +
3390 VAL* 1.3 77.9 - - - +
3410 ILE* 1.3 69.0 + - + +
3430 GLY* 3.0 4.3 + - - -
3440 SER* 2.9 34.0 + - - -
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Residues in contact with ILE 341 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250 ASP* 3.5 28.7 - - - +
260 ALA* 4.9 0.7 - - + -
1440 ALA* 4.5 6.5 - - + +
3340 GLU* 3.7 41.7 - - + +
3370 TYR* 2.9 35.5 + - + +
3380 SER* 3.6 5.2 - - - +
3400 TRP* 1.3 84.1 - - + +
3420 GLY* 1.3 57.5 + - - +
3440 SER* 3.0 7.3 + - - -
3450 ILE* 3.0 46.3 + - + +
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Residues in contact with GLY 342 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1400 LEU* 3.4 32.3 - - - +
1430 TYR* 3.7 6.9 - - - -
1440 ALA* 3.5 15.1 - - - +
3380 SER 2.8 10.7 + - - -
3390 VAL 3.4 1.5 + - - -
3410 ILE* 1.3 75.4 - - - +
3430 GLY* 1.3 54.2 + - - +
3450 ILE* 3.8 3.1 - - - +
3460 LEU* 3.1 30.0 + - - +
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Residues in contact with GLY 343 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90 VAL* 3.9 14.8 - - - -
1040 LEU* 4.3 7.1 - - - +
1400 LEU* 3.8 18.6 - - - +
3390 VAL 3.2 8.6 + - - -
3400 TRP 3.0 8.2 + - - -
3420 GLY* 1.3 75.2 - - - +
3440 SER* 1.3 53.9 + - - +
3460 LEU* 3.8 2.1 - - - +
3470 ALA* 2.8 38.3 + - - +
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Residues in contact with SER 344 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90 VAL* 3.9 10.7 - - - +
210 PHE 3.7 2.3 + - - -
220 ALA* 3.4 4.7 - - - +
230 GLY 2.8 28.2 + - - -
240 ASP 3.0 15.6 + - - -
3400 TRP* 2.9 29.6 + - - -
3410 ILE* 3.3 10.5 - - - -
3430 GLY* 1.3 72.5 - - - +
3450 ILE* 1.3 57.7 + - - +
3480 SER* 2.7 36.6 + - - -
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Residues in contact with ILE 345 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1430 TYR* 3.5 29.2 - - + +
1440 ALA* 4.4 19.1 - - - +
3410 ILE* 3.0 40.6 + - + +
3420 GLY 3.8 3.4 - - - +
3440 SER* 1.3 72.2 - - - +
3460 LEU* 1.3 66.8 + - - +
3480 SER* 2.7 21.9 + - - -
3490 LEU* 2.9 21.2 + - + +
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Residues in contact with LEU 346 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040 LEU* 4.2 12.1 - - + -
1330 TYR* 4.5 7.4 - - + +
1350 ALA* 4.7 1.3 - - + -
1400 LEU* 3.7 25.1 - - + -
1430 TYR* 3.8 24.2 - - + +
3420 GLY 3.1 13.8 + - - +
3430 GLY 3.8 1.3 - - - +
3450 ILE* 1.3 80.2 - - - +
3470 ALA* 1.3 61.7 + - - +
3490 LEU* 3.1 24.5 + - + +
3520 PHE* 3.2 48.2 - - + +
3550 MET* 5.5 3.4 - - + -
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Residues in contact with ALA 347 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30 ASP 5.7 0.2 - - - +
70 ALA* 4.3 7.7 - - + +
90 VAL* 4.5 2.0 - - + -
220 ALA* 3.9 15.7 - - + -
1040 LEU* 4.2 17.3 - - + -
3430 GLY 2.8 22.5 + - - +
3460 LEU* 1.3 74.4 - - - +
3480 SER* 1.3 59.6 + - - +
3490 LEU* 4.3 3.7 - - - +
3520 PHE* 3.9 12.7 - - - +
3560 TRP* 4.1 29.6 + - + -
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Residues in contact with SER 348 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40 GLU* 5.0 19.6 - - - +
70 ALA* 5.7 0.2 - - - -
220 ALA* 3.9 7.4 - - - +
230 GLY* 4.0 20.3 + - - -
3440 SER 2.7 23.6 + - - -
3450 ILE* 2.7 14.9 + - - -
3470 ALA* 1.3 76.9 - - - +
3490 LEU* 1.3 65.5 + - - +
3500 SER* 3.6 1.6 + - - -
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Residues in contact with LEU 349 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1430 TYR* 4.2 19.5 - - - +
3450 ILE* 2.9 23.4 + - + +
3460 LEU* 3.1 19.4 + - + +
3470 ALA 4.3 2.4 - - - +
3480 SER* 1.3 80.4 + - - +
3500 SER* 1.3 78.4 - - - +
3510 THR* 3.2 28.5 - - - +
3520 PHE* 3.3 19.1 + - + +
3530 GLN* 4.2 4.5 + - - +
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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
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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