Contacts of the strand formed by residues 341 - 345 (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 VAL 341 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3333 LEU* 5.9 5.4 - - + -
3363 ALA* 4.4 7.2 - - + -
3373 ARG 4.0 13.0 - - - +
3383 GLY* 3.8 7.3 + - - +
3393 GLU 3.6 0.4 - - - -
3403 GLU* 1.3 77.5 - - - +
3423 GLY* 1.3 67.2 + - - +
3433 LEU* 5.1 5.1 - - + +
3643 LEU* 4.1 20.6 - - + +
3663 THR* 2.5 33.6 + - - +
3683 HIS* 3.7 1.5 - - - -
5653 TYR* 3.4 26.5 - - + +
5663 ALA* 5.2 2.2 - - - +
5673 TYR* 6.1 1.1 - - + -
6443 LEU* 6.4 2.7 - - + -
6483 LEU* 4.0 26.0 - - + -
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Residues in contact with GLY 342 (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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3403 GLU 3.7 0.6 + - - -
3413 VAL* 1.3 77.9 - - - +
3433 LEU* 1.3 69.1 + - - +
3443 TYR* 3.9 18.6 - - - -
3683 HIS* 3.3 16.4 - - - -
5633 ALA* 4.1 0.6 - - - +
5653 TYR 2.9 14.5 + - - -
5663 ALA* 3.7 0.5 - - - -
5673 TYR* 3.1 23.9 + - - +
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Residues in contact with LEU 343 (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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3413 VAL* 4.3 7.4 + - + -
3423 GLY* 1.3 80.3 - - - +
3443 TYR* 1.3 61.3 + - - +
3453 LEU* 4.0 4.5 - - + +
3573 ALA* 3.4 39.3 - - + +
3603 LEU* 3.9 21.3 - - + -
3613 ALA* 4.2 10.8 - - + +
3643 LEU* 5.1 5.8 - - + -
3663 THR* 5.0 7.0 - - + -
3683 HIS 3.6 6.9 + - - -
3693 LEU* 3.1 20.3 - - + +
3703 ASP 3.0 25.8 + - - +
5493 VAL* 5.0 0.7 - - + +
5673 TYR* 4.3 9.2 - - + -
6413 LEU* 3.7 26.9 - - + -
6443 LEU* 5.4 3.1 - - + -
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Residues in contact with TYR 344 (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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3423 GLY* 3.9 16.4 - - - -
3433 LEU* 1.3 72.5 - - - +
3453 LEU* 1.3 60.7 + - - +
3683 HIS* 3.8 4.0 - - - +
3693 LEU* 4.4 4.0 - - - -
3703 ASP* 3.6 27.1 - - + -
5563 ALA* 2.9 45.5 + - - +
5573 SER 3.8 11.2 + - - -
5583 TRP* 4.1 8.7 - - - -
5603 GLU 4.4 3.1 + - - -
5633 ALA* 3.8 14.3 + - + +
5663 ALA* 3.9 16.6 - - + -
5673 TYR* 2.9 32.6 + - - +
5683 TYR* 3.3 36.5 - + + -
5693 GLY 3.1 16.6 + - - -
5703 PHE* 3.5 17.7 - - + -
5803 LYS* 4.8 0.4 - - - -
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Residues in contact with LEU 345 (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* 4.7 4.5 - - + +
3443 TYR* 1.3 76.0 - - - +
3463 ALA* 1.3 67.5 + - - +
3493 ALA* 3.9 20.0 - - + -
3533 GLU* 4.4 6.3 - - + +
3543 GLY* 4.3 7.9 - - - +
3573 ALA* 4.0 29.2 - - + -
3703 ASP 3.2 13.5 + - - +
3713 PHE* 4.2 3.1 - - + -
3723 GLN 3.1 15.3 + - - -
5443 LEU* 4.3 13.0 - - + -
5493 VAL* 4.6 7.6 - - + -
5673 TYR* 3.4 32.1 - - + +
5693 GLY* 4.5 2.9 - - - +
5703 PHE* 2.9 22.7 - - - -
6373 ALA* 5.6 3.6 - - + -
6413 LEU* 4.5 8.1 - - + -
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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