Contacts of the helix formed by residues 417 - 427 (chain 1) 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 PHE 417 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2881 GLN* 4.6 14.8 - - + -
2891 ALA* 4.1 20.2 - - + -
2991 PRO* 4.5 21.3 - - + -
3011 PRO* 4.3 22.7 - - + -
3371 MET* 4.2 19.5 - - + -
4121 GLY 4.4 2.0 - - - -
4131 SER* 3.1 29.5 + - - +
4141 LEU 3.0 1.2 + - - -
4161 HIS* 1.3 101.1 - + + +
4181 LYS* 1.3 68.2 + - - +
4191 ASP* 3.0 5.8 - - - +
4201 GLN* 2.9 37.8 + - + +
4211 TYR* 3.5 5.0 - - - -
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Residues in contact with LYS 418 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3841 VAL* 4.2 23.1 + - + -
3851 GLU* 5.3 5.1 - - - +
3881 GLU* 2.7 50.3 + - - +
4131 SER 3.3 0.6 + - - -
4141 LEU* 2.6 36.3 + - + +
4161 HIS 3.8 0.6 - - - -
4171 PHE* 1.3 70.1 - - - +
4191 ASP* 1.3 69.4 + - - +
4211 TYR* 3.0 31.4 + - + +
4221 LEU* 3.3 20.2 + - + +
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Residues in contact with ASP 419 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4161 HIS 4.8 6.1 - - - +
4171 PHE* 4.5 4.7 - - - +
4181 LYS* 1.3 80.0 + - - +
4201 GLN* 1.3 63.9 + - - +
4221 LEU* 3.0 21.2 + - + +
4231 ALA* 3.0 20.1 + - - +
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Residues in contact with GLN 420 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2881 GLN* 4.0 13.4 + - - +
3331 GLU 5.4 2.4 + - - -
3361 SER* 3.0 34.0 + - - +
3371 MET* 3.1 40.4 - - + +
3381 VAL* 4.4 3.8 - - + +
4171 PHE* 2.9 22.8 + - + +
4191 ASP* 1.3 77.2 - - - +
4211 TYR* 1.3 69.0 + - + +
4231 ALA* 3.0 23.0 + - + +
4241 LEU* 3.2 9.9 + - + +
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Residues in contact with TYR 421 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3371 MET* 5.5 1.6 - - + -
3381 VAL* 3.8 29.1 - - + +
3411 MET* 3.6 13.7 - - + +
3711 PHE* 3.5 29.7 - + - -
3741 ILE* 4.2 20.6 - - + +
3841 VAL* 3.9 25.0 - - + +
3871 LEU* 4.1 10.5 - - + -
4101 VAL* 3.8 1.0 - - - +
4131 SER* 2.3 49.2 + - - -
4141 LEU* 3.5 16.4 - - + +
4171 PHE* 3.5 8.1 - - + -
4181 LYS* 3.0 19.9 + - + +
4201 GLN* 1.3 80.4 - - + +
4221 LEU* 1.3 63.9 + - - +
4241 LEU* 3.0 4.2 + - - +
4251 ALA* 2.8 19.2 + - - +
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Residues in contact with LEU 422 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3811 GLU* 4.0 28.0 - - + +
3841 VAL* 3.6 28.3 - - + -
3851 GLU* 6.0 1.1 - - + -
4181 LYS* 3.7 23.3 - - + +
4191 ASP* 3.0 24.8 + - + +
4211 TYR* 1.3 78.9 - - - +
4231 ALA* 1.3 51.7 + - - +
4251 ALA* 3.0 7.3 + - - +
4261 ARG* 2.5 64.6 + - - +
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Residues in contact with ALA 423 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4191 ASP 3.0 10.3 + - - +
4201 GLN* 3.1 15.5 - - + +
4221 LEU* 1.3 75.5 - - - +
4241 LEU* 1.3 58.7 + - + +
4261 ARG* 2.9 4.6 + - - +
4271 GLU* 2.7 59.3 + - - +
4291 ARG* 5.3 0.2 - - - +
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Residues in contact with LEU 424 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3361 SER* 4.3 12.8 - - - +
3381 VAL* 3.9 20.9 - - + -
3741 ILE* 4.3 19.1 - - + +
3751 GLY* 4.7 3.1 - - - -
3771 GLY* 5.2 0.3 - - - -
3791 GLY* 4.8 4.0 + - - +
4201 GLN* 3.2 9.0 + - + +
4211 TYR 3.0 7.4 + - - +
4231 ALA* 1.3 79.9 - - + +
4251 ALA* 1.3 58.8 + - - +
4271 GLU* 4.1 1.6 - - - +
4281 LYS* 3.4 14.6 + - - -
4291 ARG* 3.1 65.8 + - + +
4301 PRO 4.7 0.9 - - - +
4311 VAL* 3.6 35.7 - - + -
4321 PRO* 5.4 0.4 - - + -
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Residues in contact with ALA 425 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3741 ILE* 5.1 2.9 - - + +
3791 GLY* 3.4 10.5 - - - +
3801 GLU* 3.7 28.9 - - - +
3811 GLU* 3.9 4.9 - - - +
3841 VAL* 3.8 13.0 - - + -
4211 TYR 2.8 11.9 + - - +
4221 LEU* 3.1 11.4 - - - +
4241 LEU* 1.3 76.1 - - - +
4261 ARG* 1.3 55.0 - - + +
4271 GLU 3.3 0.2 + - - -
4281 LYS* 2.2 41.0 + - - +
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Residues in contact with ARG 426 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3811 GLU* 3.3 37.1 + - + +
4221 LEU* 2.5 44.5 + - + +
4231 ALA* 4.1 3.4 - - - +
4251 ALA* 1.3 76.9 - - + +
4271 GLU* 1.3 61.9 + - + +
4281 LYS* 3.1 16.2 + - - +
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Residues in contact with GLU 427 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4231 ALA* 2.7 46.7 + - - +
4241 LEU* 3.6 0.9 + - - +
4261 ARG* 1.3 75.6 - - + +
4281 LYS* 1.3 71.7 + - - +
4291 ARG* 2.9 50.8 + - + +
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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