Contacts of the strand formed by residues 4444 - 4450 (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 THR4444 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4346D TYR* 3.4 11.9 - - + +
4348D VAL* 5.2 2.2 - - + -
4434D ALA* 3.7 35.2 - - + +
4437D HIS* 3.4 11.9 - - + -
4438D ARG* 3.3 18.2 + - - -
4442D ALA 3.0 15.8 + - - -
4443D PRO* 1.3 72.8 - - - +
4445D TYR* 1.3 68.3 + - - +
4519D GLU* 3.3 12.3 + - - +
4520D TYR* 2.8 47.6 + - + -
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Residues in contact with TYR4445 (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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4346D TYR 3.0 8.9 + - - +
4347D MET* 3.3 10.5 - - + -
4348D VAL* 2.7 32.7 + - - +
4443D PRO* 4.8 6.3 - - + -
4444D THR* 1.3 84.3 - - - +
4446D MET* 1.3 61.5 + - - +
4503D PHE* 3.9 17.5 - + - -
4507D GLY 3.7 16.1 + - - -
4508D ASN* 3.3 26.0 + - - +
4509D PRO* 3.5 27.8 - - + -
4510D ASN* 4.5 1.1 + - - -
4517D TRP* 3.8 33.2 - + + +
4518D PRO 3.5 16.4 - - - -
4519D GLU* 3.5 34.3 - - + +
4520D TYR* 4.0 3.4 - - - +
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Residues in contact with MET4446 (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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4348D VAL* 3.0 26.7 - - + +
4349D GLY* 5.1 1.6 - - - -
4350D ILE* 5.5 0.7 - - + -
4430D SER* 3.7 28.3 - - - +
4431D VAL* 3.8 18.6 - - + -
4434D ALA* 3.5 26.7 - - + -
4445D TYR* 1.3 76.6 - - - +
4447D TYR* 1.3 61.3 + - - +
4517D TRP* 3.0 13.8 + - - +
4518D PRO 5.4 0.2 + - - -
4520D TYR* 3.7 32.5 - - + +
4525D GLY 4.9 0.8 + - - -
4526D TYR* 3.3 17.6 - - + +
4527D LEU 3.0 20.1 + - - -
4539D LEU* 3.8 22.7 - - + -
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Residues in contact with TYR4447 (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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4244D ILE* 5.0 0.2 - - + -
4245D SER 4.9 0.7 - - - -
4246D GLU* 3.1 38.3 - - + +
4247D SER* 4.6 0.5 + - - -
4347D MET* 4.1 12.3 - - + -
4348D VAL 3.3 3.0 + - - -
4349D GLY* 3.2 26.9 - - - -
4350D ILE* 3.0 37.6 + - - +
4351D ASN* 4.3 3.8 + - - -
4446D MET* 1.3 76.5 - - - +
4448D GLU* 1.3 63.2 + - - +
4449D PHE* 3.8 19.5 - + + -
4471D GLU* 4.2 9.6 - - + +
4500D TRP* 3.5 31.5 - + - -
4517D TRP* 3.6 20.4 - + + -
4526D TYR* 4.5 3.6 - - - -
4527D LEU 3.1 14.8 - - - +
4529D ILE* 3.9 18.4 - - + -
4539D LEU* 4.2 5.0 - - - +
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Residues in contact with GLU4448 (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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4350D ILE* 3.2 17.5 - - + +
4352D LYS* 3.6 46.2 + - + +
4447D TYR* 1.3 75.6 - - - +
4449D PHE* 1.3 62.4 + - - +
4450D GLN* 3.9 2.6 + - + +
4526D TYR* 3.9 24.9 + - + -
4527D LEU 2.9 5.5 + - - -
4528D GLN* 3.5 11.0 + - + +
4529D ILE 2.9 23.3 + - - +
4539D LEU* 3.7 24.2 - - + +
4540D LYS* 4.2 16.5 + - - -
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Residues in contact with PHE4449 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4350D ILE 2.8 10.0 + - - +
4351D ASN* 3.2 24.2 - - - +
4352D LYS* 2.7 30.0 + - - +
4447D TYR* 3.8 10.7 - + + -
4448D GLU* 1.3 70.4 - - - +
4450D GLN* 1.3 58.0 + - - +
4451D TYR* 3.7 32.1 - + + -
4466D GLY* 4.0 2.1 - - - -
4470D ASP* 3.6 19.5 - - + -
4471D GLU* 3.6 42.6 - - + -
4474D SER* 3.9 22.0 - - - -
4492D LEU* 4.1 9.2 - - + -
4496D VAL* 4.8 3.1 - - + -
4500D TRP* 6.5 0.4 - + - -
4529D ILE* 3.5 35.2 - - + -
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Residues in contact with GLN4450 (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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4352D LYS* 3.6 48.7 - - + +
4448D GLU* 5.0 3.6 - - + +
4449D PHE* 1.3 74.3 - - - +
4451D TYR* 1.3 64.1 + - - +
4465D ILE* 3.8 19.2 - - + +
4466D GLY* 4.3 1.1 - - - -
4528D GLN* 6.2 2.0 - - - +
4529D ILE 2.8 13.3 + - - +
4530D GLY* 3.4 15.8 - - - -
4531D ALA 4.3 1.9 + - - -
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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