Contacts of the helix formed by residues 420 - 429 (chain 1) in PDB entry 6AH0
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 420 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4181 PRO* 3.1 1.2 - - - +
4191 ALA* 1.3 75.4 - - - +
4211 TYR* 1.3 58.7 + - - +
4231 PRO* 3.5 1.2 - - - +
4241 ILE* 2.9 24.9 + - - -
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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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4171 PRO* 5.2 1.3 - - - -
4181 PRO* 3.1 15.7 + - - +
4201 GLY* 1.3 70.6 - - - +
4221 VAL* 1.3 57.6 + - - +
4231 PRO 2.9 4.7 - - - -
4241 ILE* 3.1 4.9 + - - -
4251 ARG* 2.9 22.2 + - - -
365 TYR* 6.5 0.9 - - - -
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Residues in contact with VAL 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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4171 PRO 5.7 0.4 - - - -
4181 PRO 2.3 27.2 + - - -
4191 ALA* 3.9 2.9 - - - +
4211 TYR* 1.3 66.8 - - - +
4231 PRO* 1.3 56.0 - - - +
4251 ARG* 3.6 6.1 - - - +
4261 THR* 2.8 21.0 + - - -
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Residues in contact with PRO 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 ALA 2.9 23.1 - - - +
4201 GLY* 3.2 2.4 - - - +
4211 TYR 2.9 1.0 - - - -
4221 VAL* 1.3 74.5 - - - +
4241 ILE* 1.3 53.6 + - - +
4251 ARG 3.1 1.1 - - - -
4261 THR* 2.9 3.8 + - - +
4271 PRO* 2.4 33.6 - - - +
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Residues in contact with ILE 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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4201 GLY 2.9 13.9 + - - -
4211 TYR 3.1 3.3 + - - -
4231 PRO* 1.3 72.6 - - - +
4251 ARG* 1.3 51.4 + - - +
4271 PRO* 2.8 5.4 - - - -
4281 ALA* 2.4 36.4 + - - -
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Residues in contact with ARG 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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4211 TYR 2.9 13.1 + - - -
4221 VAL* 3.8 6.7 - - - +
4231 PRO 3.1 0.2 - - - -
4241 ILE* 1.3 73.7 - - - +
4261 THR* 1.3 54.6 + - - +
4281 ALA* 2.7 24.1 + - - +
4291 ARG 4.1 1.2 + - - -
405 GLY* 6.4 1.3 - - - -
445 PRO* 4.0 13.1 - - - +
455 ILE* 5.0 11.7 - - - +
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Residues in contact with THR 426 (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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4221 VAL 2.8 18.9 + - - -
4231 PRO* 2.9 6.2 + - - -
4251 ARG* 1.3 71.5 - - - +
4271 PRO* 1.3 59.5 - - - +
4281 ALA 3.6 0.2 + - - -
4291 ARG 4.6 2.9 + - - -
4301 LYS* 5.0 2.8 + - - -
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Residues in contact with PRO 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 PRO 2.4 18.7 - - - +
4241 ILE* 2.8 7.4 - - - +
4261 THR* 1.3 73.8 - - - +
4281 ALA* 1.3 54.3 + - - +
4291 ARG 3.3 0.6 + - - -
4301 LYS* 3.4 3.1 + - - +
4311 LEU* 2.6 36.1 + - - -
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Residues in contact with ALA 428 (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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4241 ILE 2.4 21.5 + - - -
4251 ARG* 2.7 15.9 + - - +
4271 PRO* 1.3 64.3 - - - +
4291 ARG* 1.3 47.3 - - - +
4311 LEU 2.7 4.7 - - - -
4321 THR* 2.2 38.6 + - - -
405 GLY 5.2 7.2 - - - -
435 GLY* 5.0 3.6 - - - -
445 PRO* 4.6 10.3 - - - -
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Residues in contact with ARG 429 (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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4251 ARG 4.1 3.2 + - - -
4261 THR 4.6 2.4 + - - -
4271 PRO 3.3 0.6 + - - -
4281 ALA* 1.3 70.9 - - - +
4301 LYS* 1.3 57.3 + - - +
4321 THR* 2.5 22.9 + - - +
4331 ALA* 3.0 10.9 + - - -
435 GLY* 5.6 1.6 - - - -
445 PRO* 4.2 13.2 - - - +
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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