Contacts of the helix formed by residues 321 - 334 (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 321 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3093 PRO* 4.6 0.2 - - - -
3203 ALA* 1.3 76.8 - - - +
3223 TRP* 1.3 69.3 + - + +
3233 GLU* 3.9 23.1 - - + +
3243 GLU* 3.2 26.9 + - - +
3253 ALA* 2.9 23.3 + - - +
6333 GLU* 6.2 0.2 - - - -
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Residues in contact with TRP 322 (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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3093 PRO* 3.9 24.5 - - + +
3213 THR* 1.3 76.8 - - + +
3233 GLU* 1.3 58.2 + - + +
3253 ALA* 3.4 6.5 + - + +
3263 PHE* 2.9 31.8 + - - +
6023 LEU* 3.6 34.3 - - + -
6033 PRO* 4.3 14.4 - - + -
6333 GLU* 3.3 44.7 + - + +
6353 GLU* 3.6 34.5 - - + -
6403 VAL* 4.4 12.6 - - + -
6433 LEU* 4.2 26.7 - - + +
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Residues in contact with GLU 323 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3213 THR* 3.1 16.8 - - + +
3223 TRP* 1.3 77.8 - - + +
3243 GLU* 1.3 59.9 + - + +
3263 PHE* 3.3 8.4 + - - +
3273 LEU* 2.9 30.5 + - - +
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Residues in contact with GLU 324 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3113 VAL* 5.3 2.6 - - + +
3133 LYS* 4.4 17.0 + - - +
3203 ALA* 4.7 9.4 - - + +
3213 THR* 3.2 29.9 + - - +
3233 GLU* 1.3 76.9 - - + +
3253 ALA* 1.3 66.4 + - - +
3273 LEU* 3.2 15.0 + - + +
3283 ALA* 3.0 24.1 + - - +
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Residues in contact with ALA 325 (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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3093 PRO* 4.9 11.2 - - + -
3103 LEU 5.5 0.9 - - - +
3113 VAL* 5.0 7.6 - - + -
3203 ALA* 4.6 12.0 - - + +
3213 THR 2.9 15.9 + - - +
3223 TRP* 3.7 9.9 - - + +
3243 GLU* 1.3 76.3 - - - +
3263 PHE* 1.3 56.6 + - - +
3283 ALA* 3.3 8.3 + - - +
3293 LEU* 2.9 32.0 + - + +
6003 VAL* 4.9 17.5 - - + +
6023 LEU* 5.3 8.1 - - + -
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Residues in contact with PHE 326 (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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3223 TRP 2.9 18.1 + - - +
3233 GLU* 3.7 6.1 - - - +
3253 ALA* 1.3 74.7 - - - +
3273 LEU* 1.3 60.6 + - + +
3293 LEU* 3.5 24.2 - - + -
3303 LYS* 2.9 76.6 + - + +
6433 LEU* 3.3 52.3 - - + -
6463 GLU* 4.1 17.5 - - + -
6473 ALA* 4.2 7.9 - - + -
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Residues in contact with LEU 327 (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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3233 GLU 2.9 15.5 + - - +
3243 GLU* 3.2 16.8 + - + +
3263 PHE* 1.3 77.2 - - + +
3283 ALA* 1.3 63.7 + - - +
3303 LYS* 3.2 24.8 + - + +
3313 GLU* 3.0 23.3 + - - +
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Residues in contact with ALA 328 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3113 VAL* 4.2 22.0 - - + -
3243 GLU 3.0 12.4 + - - +
3253 ALA 3.6 7.9 - - - +
3273 LEU* 1.3 75.8 - - - +
3293 LEU* 1.3 53.0 + - - +
3313 GLU* 3.8 5.1 - - - +
3323 GLY* 2.9 31.7 + - - -
5823 PHE* 4.4 7.5 - - + -
6003 VAL* 5.1 6.3 - - + -
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Residues in contact with LEU 329 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3253 ALA* 2.9 15.8 + - + +
3263 PHE* 3.2 34.3 - - + +
3283 ALA* 1.3 75.1 - - - +
3303 LYS* 1.3 65.5 + - - +
3323 GLY 3.5 0.2 + - - -
3333 LEU* 3.0 34.6 + - + +
5823 PHE* 4.5 9.4 - - + -
5843 VAL* 3.9 22.4 - - + -
6003 VAL* 4.9 11.2 - - + +
6023 LEU* 5.7 6.7 - - + -
6403 VAL 5.6 0.4 - - - +
6433 LEU* 4.1 8.1 - - + +
6443 LEU* 3.6 48.5 - - + +
6473 ALA* 3.8 2.4 - - + +
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Residues in contact with LYS 330 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3263 PHE* 2.9 59.8 + - + +
3273 LEU* 3.5 25.3 - - + +
3293 LEU* 1.3 72.3 - - - +
3313 GLU* 1.3 58.6 + - - +
3333 LEU 3.8 0.2 - - - -
3343 LYS* 2.9 33.7 + - - +
6463 GLU 5.3 4.9 - - - -
6473 ALA* 3.6 17.9 - - + +
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Residues in contact with GLU 331 (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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3273 LEU 3.0 15.4 + - - +
3283 ALA* 4.0 6.1 - - - +
3303 LYS* 1.3 79.3 - - - +
3323 GLY* 1.3 62.3 + - - +
3343 LYS* 3.5 41.0 + - - +
3353 GLU* 4.8 1.2 + - - +
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Residues in contact with GLY 332 (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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3283 ALA 2.9 17.4 + - - -
3293 LEU 4.0 0.9 - - - -
3303 LYS 3.3 0.2 - - - -
3313 GLU* 1.3 78.5 - - - +
3333 LEU* 1.3 66.6 + - - +
3343 LYS 3.9 0.2 + - - -
3353 GLU* 5.0 2.1 + - - +
5653 TYR* 4.1 17.3 - - - -
5823 PHE* 4.7 18.9 - - - +
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Residues in contact with LEU 333 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3293 LEU* 3.0 22.5 + - + +
3303 LYS 3.8 0.7 - - - -
3323 GLY* 1.3 79.9 - - - +
3343 LYS* 1.3 64.7 + - - +
3353 GLU 3.3 2.7 - - - -
3363 ALA* 3.2 12.3 - - + +
3413 VAL* 5.9 5.4 - - + -
5653 TYR* 4.3 22.4 - - + -
5823 PHE* 3.6 29.2 - - + -
5843 VAL* 6.0 1.6 - - + -
6443 LEU* 3.8 42.8 - - + +
6473 ALA* 4.2 9.6 - - + -
6483 LEU* 3.1 37.4 - - + +
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Residues in contact with LYS 334 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3303 LYS 2.9 18.1 + - - +
3313 GLU* 3.5 39.2 + - - +
3333 LEU* 1.3 78.4 - - - +
3353 GLU* 1.3 82.9 + - + +
3363 ALA 3.3 5.5 + - - +
6473 ALA 4.4 8.5 - - - -
6483 LEU* 5.3 0.7 - - - +
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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