Contacts of the helix formed by residues 636 - 646 (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 GLY 636 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3533 GLU* 5.0 3.1 - - - -
5863 HIS* 4.2 1.8 - - - -
6053 PRO* 4.3 15.3 - - - +
6103 LYS* 5.9 3.1 - - - -
6353 GLU* 1.3 81.7 + - - +
6373 ALA* 1.3 64.2 + - - -
6383 LEU* 3.0 8.5 - - - -
6393 GLN* 3.0 15.6 + - - +
6403 VAL* 3.0 10.2 + - - +
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Residues in contact with ALA 637 (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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3453 LEU* 5.6 3.4 - - + -
3533 GLU* 3.8 28.5 + - + +
5673 TYR* 3.2 24.7 - - + +
5863 HIS* 3.3 18.2 - - + +
6363 GLY* 1.3 70.3 - - - -
6383 LEU* 1.3 57.0 + - - +
6403 VAL* 3.8 3.4 - - - -
6413 LEU* 2.9 40.4 + - + +
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Residues in contact with LEU 638 (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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3523 GLU* 3.8 41.1 - - + +
3533 GLU* 4.0 16.8 + - + +
3563 LEU* 3.5 31.6 - - + +
6363 GLY* 4.2 2.9 - - - +
6373 ALA* 1.3 78.6 - - - +
6393 GLN* 1.3 57.7 + - - +
6413 LEU* 5.2 0.4 - - - -
6423 ALA* 3.0 28.3 + - - +
6543 PHE* 4.4 6.5 - - + -
6553 ARG 3.7 19.1 - - - +
6563 LEU 3.4 28.0 - - - +
6573 HIS* 4.5 3.1 - - + +
6603 ALA* 4.5 2.9 - - + -
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Residues in contact with GLN 639 (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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6353 GLU* 3.1 39.9 + - + +
6363 GLY 3.0 6.9 + - - +
6383 LEU* 1.3 78.8 - - - +
6403 VAL* 1.3 57.0 + - - +
6423 ALA* 3.3 7.9 + - + +
6433 LEU* 3.0 32.0 + - + +
6553 ARG* 2.8 40.2 - - - +
6563 LEU* 4.9 7.1 - - - +
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Residues in contact with VAL 640 (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* 4.4 13.2 - - + -
3293 LEU* 5.6 0.3 - - - +
5673 TYR* 4.1 25.4 - - + -
5863 HIS* 3.7 19.5 - - + +
6023 LEU* 4.9 15.5 - - + -
6353 GLU* 3.6 24.2 - - + +
6363 GLY 3.0 16.7 + - - +
6373 ALA* 3.9 6.5 - - - +
6393 GLN* 1.3 73.9 - - - +
6413 LEU* 1.3 60.5 + - - +
6433 LEU* 3.2 10.0 + - + +
6443 LEU* 2.8 36.3 + - + +
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Residues in contact with LEU 641 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3433 LEU* 3.7 30.1 - - + -
3453 LEU* 4.5 11.4 - - + -
3533 GLU* 4.8 7.4 - - + +
3563 LEU* 4.1 19.1 - - + -
3573 ALA* 4.2 24.2 - - + +
3603 LEU* 4.2 14.8 - - + +
5673 TYR* 4.0 22.7 - - + -
6373 ALA* 2.9 24.8 + - + +
6383 LEU 3.9 2.7 - - - +
6403 VAL* 1.3 72.9 - - - +
6423 ALA* 1.3 67.9 + - - +
6443 LEU* 3.8 14.1 - - + +
6453 ALA* 2.9 26.9 + - - +
6523 PRO* 4.9 0.8 - - - +
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Residues in contact with ALA 642 (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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3563 LEU* 4.6 1.0 - - - +
6383 LEU 3.0 19.1 + - - +
6393 GLN* 3.5 8.5 - - + +
6403 VAL 3.3 0.2 - - - -
6413 LEU* 1.3 77.3 - - - +
6433 LEU* 1.3 61.1 + - - +
6463 GLU* 3.4 18.8 + - - +
6523 PRO* 3.2 35.6 - - + +
6543 PHE 3.5 21.3 - - - +
6553 ARG* 4.0 14.1 - - + -
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Residues in contact with LEU 643 (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* 4.2 30.3 - - + +
3263 PHE* 3.3 59.7 - - + -
3293 LEU* 4.5 5.8 - - + -
6023 LEU* 6.1 1.6 - - + -
6393 GLN 3.0 16.7 + - - +
6403 VAL* 3.2 6.3 + - + +
6423 ALA* 1.3 75.0 - - - +
6443 LEU* 1.3 63.1 + - - +
6453 ALA 3.4 0.2 - - - -
6463 GLU* 3.4 27.7 - - - +
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Residues in contact with LEU 644 (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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3293 LEU* 3.6 40.4 - - + +
3333 LEU* 3.8 21.1 - - + +
3413 VAL* 6.4 2.0 - - + -
3433 LEU* 5.4 2.7 - - + -
5673 TYR* 4.0 39.7 - - + -
5843 VAL* 4.4 11.9 - - + -
6403 VAL* 2.8 20.2 + - + +
6413 LEU* 3.2 17.9 + - + +
6433 LEU* 1.3 76.6 - - - +
6453 ALA* 1.3 63.7 + - - +
6463 GLU 3.2 0.4 - - - -
6473 ALA* 3.6 14.9 + - - +
6483 LEU* 4.2 6.1 + - + +
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Residues in contact with ALA 645 (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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3603 LEU* 3.6 32.7 - - + +
6413 LEU 2.9 16.2 + - - +
6423 ALA 4.2 4.3 - - - +
6443 LEU* 1.3 74.1 - - - +
6463 GLU* 1.3 60.6 + - - +
6473 ALA 3.2 0.9 - - - -
6483 LEU* 2.9 25.8 + - + +
6493 GLY 3.2 5.5 + - - -
6503 VAL* 3.2 26.9 + - + +
6523 PRO* 4.3 7.4 - - + -
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Residues in contact with GLU 646 (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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3263 PHE* 4.1 14.0 - - + -
3303 LYS* 5.3 3.5 - - - -
6423 ALA 3.4 13.2 + - - +
6433 LEU* 3.4 39.9 + - - +
6443 LEU 3.2 1.2 - - - -
6453 ALA* 1.3 78.6 - - - +
6473 ALA* 1.3 59.9 + - - +
6483 LEU 3.3 0.5 + - - -
6493 GLY* 3.5 9.4 + - - +
6503 VAL 4.2 4.3 - - - +
6523 PRO* 4.6 11.7 - - + -
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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