Contacts of the strand formed by residues 4242 - 4246 (chain D) in PDB entry 2H7C
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 ARG4242 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4214D SER* 4.0 10.8 + - - -
4215D VAL 3.4 3.0 + - - -
4216D THR* 3.3 19.4 - - + +
4217D ILE 3.1 22.0 + - - -
4240D PHE* 3.6 8.2 - - - -
4241D HIS* 1.3 107.5 + - - +
4243D ALA* 1.3 63.5 + - - +
4344D VAL* 4.1 2.7 - - - +
4345D PRO* 3.5 24.4 - - + +
4503D PHE* 3.7 24.7 + - + +
4504D ALA 2.7 24.1 + - - -
4505D ARG 3.1 23.0 + - - -
4506D ASN* 3.5 13.7 + - - +
4507D GLY* 3.8 12.3 - - - -
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Residues in contact with ALA4243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4217D ILE* 3.3 11.0 - - + -
4227D VAL* 3.7 17.3 - - + -
4231D VAL* 3.9 15.7 - - + -
4240D PHE* 4.3 4.3 - - + -
4242D ARG* 1.3 77.0 - - - +
4244D ILE* 1.3 64.0 + - - +
4344D VAL* 4.3 2.5 - - + -
4345D PRO 3.1 8.8 + - - +
4346D TYR* 3.4 18.6 - - + -
4347D MET 2.8 24.1 + - - -
4503D PHE* 3.3 6.6 - - - -
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Residues in contact with ILE4244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4136D MET* 4.6 2.0 - - + -
4216D THR* 4.3 10.8 - - + -
4217D ILE 2.9 8.3 + - - -
4218D PHE* 3.2 34.0 - - + -
4219D GLY 3.3 6.8 + - - -
4227D VAL* 3.8 6.3 - - - +
4243D ALA* 1.3 81.4 - - - +
4245D SER* 1.3 64.5 + - - +
4246D GLU* 4.0 26.5 - - + +
4347D MET* 3.2 31.0 - - + +
4447D TYR* 5.0 0.7 - - + -
4500D TRP* 3.7 36.8 - - + +
4503D PHE* 3.7 26.9 - - + -
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Residues in contact with SER4245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4219D GLY 4.0 2.5 - - - -
4224D GLY* 2.9 20.3 + - - -
4227D VAL* 3.6 5.9 - - - +
4228D SER* 4.0 0.2 - - - -
4244D ILE* 1.3 73.3 - - - +
4246D GLU* 1.3 61.9 + - - +
4247D SER 3.9 0.4 + - - -
4248D GLY 3.4 16.9 + - - -
4249D VAL* 4.1 7.6 - - - -
4346D TYR* 2.7 33.7 + - - -
4347D MET 2.8 10.0 + - - +
4348D VAL* 3.5 4.0 - - - +
4349D GLY 3.0 25.6 + - - +
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Residues in contact with GLU4246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4138D TRP* 3.8 9.7 - - - -
4218D PHE* 3.8 16.6 - - - +
4219D GLY 2.9 15.7 + - - +
4220D GLU* 3.1 3.6 - - - +
4221D SER 2.8 31.4 + - - -
4224D GLY* 4.2 1.1 - - - -
4244D ILE* 4.0 12.2 - - + +
4245D SER* 1.3 73.0 - - - +
4247D SER* 1.3 59.4 + - - +
4248D GLY 3.4 0.8 + - - -
4447D TYR* 3.1 23.8 - - + +
4471D GLU* 2.8 39.2 - - - +
4472D LEU* 3.9 11.8 - - - +
4475D VAL* 4.0 5.1 - - - +
4500D TRP* 3.0 28.8 + - + -
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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