Contacts of the helix formed by residues 336 - 351 (chain 1) in PDB entry 6Q8O
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 336 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2881 GLN* 3.8 1.1 - - - +
3331 GLU 4.5 1.5 + - - -
3351 VAL* 1.3 79.5 - - - +
3371 MET* 1.3 66.7 + - - +
3381 VAL* 3.7 7.2 + - - +
3391 ASP* 3.0 14.8 + - - +
3401 ALA* 3.5 7.6 + - - +
4201 GLN* 2.5 38.8 + - - +
4241 LEU* 4.4 9.7 - - - +
4311 VAL* 4.8 7.4 - - - -
4321 PRO* 3.6 33.1 - - - +
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Residues in contact with MET 337 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2881 GLN* 3.7 12.7 - - + +
2891 ALA* 3.1 35.2 - - + -
2991 PRO* 4.7 12.1 - - + -
3311 ILE* 3.9 25.1 - - + -
3361 SER* 1.3 74.4 + - - +
3381 VAL* 1.3 64.8 + - + +
3401 ALA* 3.1 5.2 + - - +
3411 MET* 2.9 55.9 + - + +
4131 SER* 4.9 2.9 - - - +
4171 PHE* 3.7 46.0 - - + -
4201 GLN* 3.8 14.7 - - + +
4211 TYR* 5.3 4.3 - - + +
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Residues in contact with VAL 338 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3361 SER* 3.1 4.7 + - - +
3371 MET* 1.3 76.3 - - + +
3391 ASP* 1.3 56.6 + - - +
3411 MET* 3.8 3.8 - - - -
3421 TRP* 2.8 35.5 + - + +
3711 PHE* 4.1 18.0 - - + +
3741 ILE* 4.8 3.8 - - + -
3751 GLY* 4.0 15.5 - - - +
4201 GLN* 5.2 2.0 - - + -
4211 TYR* 3.6 41.7 - - + +
4241 LEU* 3.5 28.0 - - + -
4311 VAL* 3.6 17.5 - - + -
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Residues in contact with ASP 339 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3351 VAL* 3.3 22.7 - - + +
3361 SER 3.0 10.7 + - - +
3381 VAL* 1.3 79.2 - - - +
3401 ALA* 1.3 62.5 + - - +
3421 TRP* 3.1 9.9 - - - +
3431 ASN 3.0 18.9 + - - -
4311 VAL* 3.8 30.3 - - + +
4321 PRO 4.9 2.0 - - - +
4331 ARG* 3.2 33.8 + - - -
892 LYS* 3.1 32.3 + - - +
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Residues in contact with ALA 340 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3311 ILE* 3.6 33.2 - - + -
3351 VAL* 4.8 2.6 - - + +
3361 SER 3.5 3.4 + - - +
3371 MET* 3.1 10.8 + - - +
3391 ASP* 1.3 79.8 + - - +
3411 MET* 1.3 61.1 + - - +
3431 ASN* 3.2 4.2 + - - -
3441 LEU* 2.9 31.8 + - + +
862 LEU* 3.6 26.3 - - + +
892 LYS* 5.4 1.8 - - - -
902 LEU* 5.2 3.4 - - + -
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Residues in contact with MET 341 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2911 ILE* 5.2 1.6 - - + -
2991 PRO* 4.7 6.5 - - + -
3311 ILE* 5.2 2.5 - - - -
3371 MET* 2.9 36.9 + - - +
3401 ALA* 1.3 74.7 - - - +
3421 TRP* 1.3 60.4 + - - +
3441 LEU* 3.4 23.1 - - + +
3451 THR* 2.9 36.8 + - - +
3711 PHE* 3.8 22.7 - - + -
4091 PRO* 3.3 48.5 - - + +
4101 VAL* 3.8 6.7 - - + +
4131 SER* 3.7 19.3 - - - +
4211 TYR* 4.0 5.6 - - - +
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Residues in contact with TRP 342 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3381 VAL* 2.8 26.2 + - + +
3391 ASP* 3.1 15.0 - - - +
3411 MET* 1.3 75.4 - - - +
3431 ASN* 1.3 59.1 + - + +
3451 THR* 2.9 21.4 + - - -
3461 ARG* 2.9 54.1 + - + -
3681 VAL* 3.9 14.1 - - + -
3711 PHE* 2.9 45.3 + - + -
3721 ALA* 3.1 30.0 + - + +
3751 GLY* 4.9 6.3 - - - -
3761 THR* 5.1 1.0 + - - -
4311 VAL* 5.6 2.7 - - + -
892 LYS* 5.1 2.7 - - - +
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Residues in contact with ASN 343 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3391 ASP 3.0 3.7 + - - +
3401 ALA* 3.8 6.3 - - - +
3421 TRP* 1.3 79.6 - - - +
3441 LEU* 1.3 57.7 + - - +
3461 ARG* 3.1 24.3 - - - +
3471 PHE* 2.9 28.4 + - - +
842 ALA* 2.6 25.6 + - - +
852 THR* 3.2 12.9 - - - +
862 LEU* 3.1 24.6 + - - +
892 LYS* 3.2 31.6 - - + +
942 GLU* 3.8 7.5 + - - -
1232 GLU* 5.0 0.9 - - - +
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Residues in contact with LEU 344 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981 PRO* 6.0 3.4 - - + -
2911 ILE* 4.2 17.5 - - + -
2951 SER* 4.3 24.0 - - - +
3401 ALA 2.9 16.3 + - - +
3411 MET* 3.4 40.4 - - + +
3431 ASN* 1.3 77.0 - - - +
3451 THR* 1.3 60.1 + - + +
3471 PHE* 3.2 9.6 + - + +
3481 TYR* 2.9 40.1 + - + -
4091 PRO* 4.5 12.6 - - + -
4101 VAL* 6.3 0.2 - - + -
852 THR* 6.0 1.3 - - + -
862 LEU* 3.8 34.1 - - + +
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Residues in contact with THR 345 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3411 MET 2.9 21.9 + - - +
3421 TRP* 2.9 21.7 + - - -
3441 LEU* 1.3 73.5 - - + +
3461 ARG* 1.3 56.9 + - - +
3481 TYR* 3.8 9.4 - - + +
3491 ALA* 2.9 30.3 + - - +
3631 VAL* 4.1 9.2 - - + +
3671 MET* 5.3 7.4 - - + -
3681 VAL* 3.6 26.8 - - - +
3711 PHE* 4.0 15.3 - - + -
4061 ALA* 5.0 6.1 - - + +
4101 VAL* 3.9 26.5 - - + -
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Residues in contact with ARG 346 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3421 TRP* 2.9 46.3 + - + +
3431 ASN* 3.1 41.2 - - - +
3451 THR* 1.3 76.7 + - - +
3471 PHE* 1.3 57.7 + - - +
3491 ALA* 3.8 4.8 - - - +
3501 HIS* 2.9 31.0 + - - +
3681 VAL* 3.9 9.4 - - + -
842 ALA* 5.0 4.8 - - - +
892 LYS* 5.5 0.7 - - - +
942 GLU* 5.9 0.4 - - - -
1212 LYS* 4.3 30.8 - - - +
1232 GLU* 4.7 14.6 + - - +
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Residues in contact with PHE 347 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961 SER 4.4 4.9 - - - -
981 PRO* 3.5 36.3 - - + -
1801 TYR* 3.9 25.1 - + + -
2951 SER* 4.3 2.9 - - - -
3431 ASN* 2.9 22.8 + - - +
3441 LEU* 3.2 11.6 + - + +
3461 ARG* 1.3 75.6 - - + +
3481 TYR* 1.3 104.7 + + - +
3501 HIS* 3.1 15.2 + - - +
3511 GLU* 3.3 20.9 + - + +
852 THR* 4.5 10.1 - - + -
1232 GLU* 3.2 52.5 - - + +
1242 CYS 4.7 0.2 - - - -
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Residues in contact with TYR 348 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971 GLU* 3.7 0.9 + - - -
1801 TYR* 4.0 23.6 - + - -
2951 SER* 2.4 51.5 + - - -
2961 SER* 3.2 4.0 + - - -
3441 LEU* 2.9 40.2 + - + +
3451 THR* 3.8 8.3 - - + +
3471 PHE* 1.3 87.1 - + - +
3491 ALA* 1.3 62.4 + - - +
3511 GLU* 3.1 14.0 + - - +
3521 SER* 3.2 13.3 + - - -
3631 VAL* 4.5 6.5 - - + +
4021 LEU* 3.6 32.6 - - + +
4051 ALA* 3.5 22.8 + - + -
4061 ALA* 4.0 23.8 - - + -
4091 PRO* 4.8 4.7 - - + -
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Residues in contact with ALA 349 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3451 THR 2.9 17.7 + - - +
3461 ARG* 3.8 7.2 - - - +
3481 TYR* 1.3 72.2 - - - +
3501 HIS* 1.3 64.9 + - - +
3511 GLU 3.0 3.5 + - - -
3521 SER* 3.5 14.7 + - - +
3631 VAL* 3.9 11.2 - - + +
3641 ALA* 3.5 39.2 - - + +
3681 VAL* 4.6 4.7 - - + -
2063 GLY* 4.5 7.3 - - - -
2073 VAL* 5.3 0.3 + - - +
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Residues in contact with HIS 350 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3461 ARG* 2.9 18.3 + - - +
3471 PHE 3.1 12.3 + - - +
3491 ALA* 1.3 76.4 - - - +
3511 GLU* 1.3 66.2 + - - +
3521 SER 3.6 0.8 + - - +
682 SER* 3.6 25.5 + - - -
1212 LYS* 5.1 11.4 + - + -
1222 VAL* 5.4 0.8 - - - -
1232 GLU* 3.4 40.5 + - + +
2053 ARG* 3.0 24.7 + - - +
2063 GLY* 5.6 1.8 - - - -
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Residues in contact with GLU 351 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1781 GLY 4.2 9.9 - - - +
1791 ALA* 3.4 6.0 - - - +
1801 TYR* 2.6 57.5 + - + -
1811 ILE* 4.1 16.8 + - - +
3471 PHE* 3.3 26.2 + - + +
3481 TYR 3.1 7.2 + - - +
3491 ALA 3.0 0.8 - - - -
3501 HIS* 1.3 96.7 - - + +
3521 SER* 1.3 65.0 + - - +
3531 CYS* 3.4 2.1 + - - -
4021 LEU* 4.5 6.8 - - + +
1232 GLU* 4.1 8.1 - - - +
2053 ARG* 3.9 17.4 + - - +
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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