Contacts of the helix formed by residues 514 - 528 (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 ASP 514 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3763 ALA* 5.2 0.2 - - - -
4713 GLY* 5.3 8.5 - - - +
4733 GLU* 6.2 0.2 - - - +
4743 ARG* 3.7 32.0 + - - +
5103 GLY 4.0 8.2 + - - +
5113 VAL* 3.1 17.7 + - - +
5123 LEU 3.4 1.5 - - - -
5133 GLN* 1.3 79.1 - - - +
5153 THR* 1.3 66.0 + - - +
5163 VAL* 3.4 4.9 + - - +
5173 ALA* 3.4 26.7 + - + +
5183 ALA* 3.2 14.8 + - - +
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Residues in contact with THR 515 (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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3763 ALA* 4.0 18.9 + - - +
3773 ALA* 4.9 5.4 - - - -
5133 GLN 4.1 1.8 + - - -
5143 ASP* 1.3 75.0 + - - +
5163 VAL* 1.3 66.5 + - + +
5183 ALA* 3.4 6.0 + - - +
5193 GLU* 2.9 28.7 + - + +
6833 LEU* 4.0 32.2 - - + +
6843 ARG 4.0 14.9 + - - -
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Residues in contact with VAL 516 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4743 ARG* 3.3 41.3 - - + +
5143 ASP* 3.4 3.4 + - - +
5153 THR* 1.3 83.5 - - + +
5173 ALA* 1.3 63.8 + - - +
5193 GLU* 3.2 6.9 + - + +
5203 ARG* 2.9 61.1 + - + +
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Residues in contact with ALA 517 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4733 GLU* 4.7 7.6 - - + +
4743 ARG* 3.9 29.1 - - + +
4773 LEU* 3.2 14.7 - - + +
5113 VAL* 4.1 20.6 - - + +
5143 ASP* 3.4 25.5 + - + +
5153 THR 3.4 0.4 - - - -
5163 VAL* 1.3 79.4 - - - +
5183 ALA* 1.3 57.5 + - - +
5203 ARG* 4.8 1.3 - - - -
5213 ALA* 2.9 24.4 + - - +
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Residues in contact with ALA 518 (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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3773 ALA* 3.4 33.7 - - + -
3813 LEU* 6.3 0.7 - - + -
3823 PHE* 3.6 16.5 - - + -
5073 LEU* 5.4 0.2 - - + -
5113 VAL* 4.1 13.3 + - + +
5123 LEU* 4.9 3.1 - - - -
5143 ASP 3.2 12.4 + - - +
5153 THR 3.8 1.8 - - - +
5173 ALA* 1.3 75.9 - - - +
5193 GLU* 1.3 61.5 + - - +
5213 ALA* 3.3 7.2 + - - +
5223 ARG* 2.9 30.1 + - - +
6833 LEU* 5.6 0.9 - - + -
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Residues in contact with GLU 519 (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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5153 THR* 2.9 20.9 + - + +
5163 VAL* 3.4 9.4 - - + +
5183 ALA* 1.3 76.5 - - - +
5203 ARG* 1.3 59.1 + - + +
5223 ARG* 3.2 43.7 + - - +
5233 LEU* 2.9 38.7 + - + +
6833 LEU* 3.1 33.2 - - + +
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Residues in contact with ARG 520 (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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4743 ARG* 2.9 50.8 + - - +
4753 GLU* 4.2 2.2 - - - +
4773 LEU* 3.9 14.4 - - + -
4783 LEU* 3.4 39.7 - - - +
4813 LEU* 3.8 22.8 - - + +
5163 VAL* 2.9 37.8 + - + +
5173 ALA 3.9 0.9 - - - +
5193 GLU* 1.3 76.0 - - + +
5213 ALA* 1.3 61.8 + - - +
5233 LEU* 3.7 8.4 - - + +
5243 LEU* 2.8 31.5 + - - +
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Residues in contact with ALA 521 (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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3823 PHE* 3.9 1.6 - - + -
4773 LEU* 3.4 16.1 - - + +
5053 LEU* 3.6 12.0 - - + +
5073 LEU* 3.7 34.8 - - + -
5173 ALA 2.9 18.1 + - - +
5183 ALA 3.5 5.8 - - - +
5193 GLU 3.3 0.2 - - - -
5203 ARG* 1.3 77.4 - - - +
5223 ARG* 1.3 62.8 + - - +
5243 LEU* 3.2 3.6 + - - +
5253 ALA* 2.9 27.9 + - - +
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Residues in contact with ARG 522 (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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3813 LEU* 3.5 41.1 - - + +
3823 PHE* 3.6 17.2 - - + -
5183 ALA 2.9 13.9 + - - +
5193 GLU* 3.3 37.4 + - - +
5213 ALA* 1.3 75.2 - - - +
5233 LEU* 1.3 76.9 + - - +
5253 ALA* 3.7 2.4 - - - +
5263 GLU* 2.9 64.3 + - + +
6813 LYS* 3.5 35.3 - - - +
6833 LEU* 5.9 0.8 - - - +
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Residues in contact with LEU 523 (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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4813 LEU* 4.3 11.4 - - + -
5193 GLU* 2.9 35.5 + - + +
5203 ARG* 3.7 12.1 - - + +
5213 ALA 3.3 0.2 - - - -
5223 ARG* 1.3 94.3 - - - +
5243 LEU* 1.3 61.8 + - - +
5263 GLU* 3.2 6.5 + - + +
5273 ARG* 3.0 62.9 + - + +
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Residues in contact with LEU 524 (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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3973 LEU* 4.3 0.9 - - + -
4773 LEU* 4.9 7.0 - - + +
4803 LEU* 4.0 41.7 - - + +
4813 LEU* 3.6 25.1 - - + +
4973 TRP* 3.3 39.2 - - + +
4983 GLU* 5.3 0.7 - - - +
5053 LEU* 4.2 26.5 - - + -
5203 ARG 2.8 21.3 + - - +
5213 ALA* 3.6 4.0 - - - +
5233 LEU* 1.3 74.5 - - - +
5253 ALA* 1.3 55.9 + - - +
5273 ARG* 4.0 2.9 - - - +
5283 LYS* 3.2 29.1 + - - +
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Residues in contact with ALA 525 (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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3823 PHE* 5.6 0.2 - - + -
3833 PRO* 5.0 5.2 - - + +
4973 TRP* 4.4 2.2 - - - -
5053 LEU* 3.7 20.6 - - + -
5213 ALA 2.9 18.9 + - - +
5223 ARG* 3.7 2.9 - - - +
5243 LEU* 1.3 69.5 - - - +
5263 GLU* 1.3 59.6 + - - +
5283 LYS 2.8 21.1 - - - +
5303 ALA* 3.0 29.4 + - + +
5323 VAL* 3.9 19.1 - - + -
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Residues in contact with GLU 526 (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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3813 LEU 4.9 3.8 - - - +
3833 PRO* 5.8 8.3 - - + -
5223 ARG* 2.9 57.6 + - + +
5233 LEU* 3.8 6.5 - - + +
5253 ALA* 1.3 80.3 - - - +
5273 ARG* 1.3 65.4 - - + +
5283 LYS 3.5 4.9 + - - +
5293 GLY* 4.4 2.4 + - - -
6793 ARG* 5.3 14.0 + - - +
6813 LYS* 6.1 0.2 - - - +
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Residues in contact with ARG 527 (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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4813 LEU* 4.1 34.1 + - - +
5233 LEU* 3.0 54.1 + - + +
5243 LEU* 4.0 3.6 - - - +
5263 GLU* 1.3 79.9 - - + +
5283 LYS* 1.3 58.1 + - - +
5293 GLY 3.8 1.4 + - - -
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Residues in contact with LYS 528 (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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4973 TRP* 3.1 39.5 - - + +
4983 GLU* 3.7 14.9 + - - +
5003 ALA 3.0 20.2 + - - -
5013 LYS* 4.3 8.5 + - - +
5033 PRO* 3.4 28.9 - - + -
5243 LEU 3.2 11.6 + - - +
5253 ALA 2.8 20.6 - - - +
5263 GLU 3.7 1.7 - - - +
5273 ARG* 1.3 77.9 - - - +
5293 GLY* 1.3 70.7 + - - +
5303 ALA* 2.8 14.6 + - + +
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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