Contacts of the helix formed by residues 350 - 364 (chain 3) in PDB entry 6Q8W
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 THR 350 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3483 ASP 4.1 7.6 - - - +
3493 ALA* 1.3 76.0 - - - +
3513 LEU* 1.3 54.7 + - - +
3523 GLU* 3.3 18.9 + - - +
3533 GLU* 2.9 39.6 + - - +
3543 GLY* 2.8 33.1 + - - -
5403 ASN* 3.3 2.3 + - - +
5443 LEU* 4.1 0.9 - - - +
6103 LYS* 4.4 13.2 - - + +
6113 ARG 4.7 3.1 - - - +
6123 GLY* 4.5 7.6 - - - -
6133 HIS 3.4 17.5 - - - +
6143 LEU* 5.5 1.1 - - + -
6243 LEU* 4.6 13.7 - - + -
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Residues in contact with LEU 351 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3503 THR* 1.3 75.1 - - - +
3523 GLU* 1.3 64.1 + - - +
3543 GLY* 5.0 0.2 - - - -
3553 LEU* 3.0 26.3 + - - +
5403 ASN* 3.7 8.7 - - - +
5433 GLY* 3.5 20.2 - - - -
5463 ALA* 6.0 0.7 - - + -
5473 MET* 3.6 23.0 - - + +
6133 HIS* 3.0 26.6 + - + +
6153 VAL* 3.4 33.7 - - + +
6213 VAL* 4.2 6.3 - - + -
6643 LEU* 4.0 21.0 - - + +
6693 VAL* 3.8 29.4 - - + -
6763 LEU* 6.1 0.7 - - + -
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Residues in contact with GLU 352 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3503 THR* 3.2 9.7 - - - +
3513 LEU* 1.3 79.3 + - - +
3533 GLU* 1.3 58.4 + - + +
3553 LEU* 3.4 4.8 + - - +
3563 LEU* 3.0 28.2 + - - +
6113 ARG 5.1 1.1 - - - +
6123 GLY* 3.5 13.5 - - - -
6133 HIS* 3.1 30.0 + - - -
6383 LEU* 3.8 15.5 - - + +
6543 PHE* 4.5 3.9 - - - -
6573 HIS* 3.7 13.2 - - + -
6603 ALA* 3.4 32.5 - - + -
6613 GLN* 2.6 29.6 + - - +
6643 LEU* 4.1 11.9 - - + -
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Residues in contact with GLU 353 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3453 LEU* 4.5 7.9 - - + -
3493 ALA* 3.3 16.6 - - + +
3503 THR* 2.9 38.0 + - - +
3523 GLU* 1.3 74.6 - - + +
3543 GLY* 1.3 66.8 + - - +
3563 LEU* 3.0 2.3 + - - +
3573 ALA* 2.9 25.6 + - - +
6103 LYS* 3.9 25.6 + - - +
6363 GLY* 4.8 1.2 - - - -
6373 ALA* 3.8 31.5 + - + +
6383 LEU* 4.0 29.9 + - + +
6413 LEU* 4.8 5.0 - - + +
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Residues in contact with GLY 354 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3453 LEU* 4.3 3.1 - - - -
3503 THR 2.8 17.0 + - - -
3513 LEU 4.0 0.9 - - - -
3533 GLU* 1.3 72.0 - - - +
3553 LEU* 1.3 56.3 + - - +
3573 ALA 3.5 0.2 + - - -
3583 SER* 2.9 30.8 + - - -
5443 LEU* 3.5 28.1 - - - +
5473 MET* 3.7 10.5 - - - -
5493 VAL* 3.5 11.1 - - - +
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Residues in contact with LEU 355 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3513 LEU 3.0 20.0 + - - +
3523 GLU* 3.7 4.3 - - - +
3543 GLY* 1.3 76.9 - - - +
3563 LEU* 1.3 58.2 + - - +
3583 SER* 3.4 3.8 + - - +
3593 GLU* 3.0 40.5 + - + +
5473 MET* 3.5 17.8 - - - +
6543 PHE* 3.4 30.5 - - + -
6633 ALA* 3.9 26.2 - - + +
6643 LEU* 4.1 13.9 - - + +
6673 ARG* 3.8 33.2 - - + +
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Residues in contact with LEU 356 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3523 GLU 3.0 16.8 + - - +
3533 GLU 3.0 3.3 + - - +
3553 LEU* 1.3 73.4 - - - +
3573 ALA* 1.3 61.9 + - - +
3593 GLU 3.5 0.9 + - - +
3603 LEU* 2.9 38.4 + - + +
6383 LEU* 3.5 43.7 - - + +
6413 LEU* 4.1 19.5 - - + -
6423 ALA 4.6 1.8 - - - +
6523 PRO* 4.3 8.7 - - + -
6533 PRO* 3.7 18.6 - - + -
6543 PHE* 3.7 47.6 - - + +
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Residues in contact with ALA 357 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3433 LEU* 3.4 28.2 - - + +
3453 LEU* 4.0 23.6 - - + -
3533 GLU 2.9 14.8 + - - +
3543 GLY* 4.0 2.9 - - - +
3563 LEU* 1.3 77.9 - - - +
3583 SER* 1.3 63.1 + - - +
3603 LEU* 3.2 2.8 + - - -
3613 ALA* 2.9 22.0 + - - +
3693 LEU* 4.4 6.3 - - + -
5493 VAL* 5.0 2.9 - - + -
6413 LEU* 4.2 14.3 - - + +
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Residues in contact with SER 358 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3543 GLY 2.9 16.3 + - - -
3553 LEU* 3.6 5.4 - - - -
3573 ALA* 1.3 75.0 - - - +
3593 GLU* 1.3 65.9 + - - +
3613 ALA* 3.0 6.2 + - - +
3623 LYS* 2.9 20.5 + - - +
3693 LEU* 4.6 9.2 - - - -
5473 MET 2.9 30.2 + - - -
5483 GLY* 4.4 10.3 + - - -
5493 VAL* 4.5 3.0 - - - +
6673 ARG* 3.9 14.0 + - - -
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Residues in contact with GLU 359 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3553 LEU* 3.0 40.6 + - + +
3563 LEU* 4.0 4.5 - - - +
3583 SER* 1.3 81.0 + - - +
3603 LEU* 1.3 58.2 + - - +
3623 LYS* 3.1 30.0 + - + +
3633 ALA* 3.0 26.9 + - - +
6533 PRO* 4.8 12.8 - - + -
6543 PHE* 4.4 14.6 - - + -
6673 ARG* 4.2 11.6 + - - -
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Residues in contact with LEU 360 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3433 LEU* 3.9 23.3 - - + -
3563 LEU* 2.9 26.2 + - + +
3573 ALA* 3.6 3.4 - - - +
3583 SER 3.1 0.2 - - - -
3593 GLU* 1.3 76.9 - - - +
3613 ALA* 1.3 53.5 + - - +
3633 ALA* 3.2 4.4 + - - +
3643 LEU* 2.4 52.0 + - + +
6413 LEU* 4.2 29.4 - - + +
6453 ALA* 3.6 32.1 - - + +
6503 VAL* 4.0 18.6 - - + -
6513 ARG 5.3 2.9 - - - +
6523 PRO* 5.4 6.3 - - + -
6533 PRO* 5.8 3.1 - - + -
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Residues in contact with ALA 361 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3433 LEU* 4.2 3.8 - - + +
3573 ALA 2.9 8.4 + - - +
3583 SER 3.6 3.1 - - - +
3603 LEU* 1.3 73.4 - - - +
3623 LYS* 1.3 65.9 + - - +
3643 LEU* 2.6 22.0 - - - +
3653 LYS* 3.8 5.2 - - - -
3663 THR* 3.6 25.8 + - + +
3693 LEU* 3.5 33.4 - - + -
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Residues in contact with LYS 362 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3583 SER 2.9 11.5 + - - +
3593 GLU* 3.1 35.5 + - - +
3613 ALA* 1.3 78.8 - - - +
3633 ALA* 1.3 66.5 + - - +
3643 LEU 4.4 0.5 - - - -
3653 LYS* 4.4 6.2 + - - +
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Residues in contact with ALA 363 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3593 GLU 3.0 11.9 + - - +
3603 LEU* 3.7 4.0 - - - +
3623 LYS* 1.3 80.3 - - + +
3643 LEU* 1.3 59.0 + - - +
3653 LYS* 3.1 16.6 + - - +
6503 VAL* 3.6 26.0 - - + -
6513 ARG 5.7 0.9 - - - +
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Residues in contact with LEU 364 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3383 GLY* 3.6 28.3 - - - +
3413 VAL* 4.1 25.6 - - + -
3433 LEU* 5.1 7.6 - - + -
3603 LEU* 2.4 34.8 + - + +
3613 ALA* 2.6 25.2 - - - +
3633 ALA* 1.3 69.1 - - - +
3653 LYS* 1.3 56.5 + - - +
3663 THR* 2.8 23.2 + - + +
6483 LEU* 3.7 26.5 - - + -
6503 VAL* 4.2 23.1 - - + +
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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