Contacts of the strand formed by residues 4525 - 4530 (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 GLY4525 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4446D MET 4.9 0.5 + - - -
4518D PRO* 3.8 23.9 - - - +
4519D GLU 4.2 8.9 + - - -
4520D TYR* 3.3 25.1 - - - +
4521D ASN* 4.7 0.2 + - - -
4523D LYS* 3.4 4.8 - - - +
4524D GLU* 1.3 79.6 - - - +
4526D TYR* 1.3 58.9 + - - -
4536D ALA 3.2 11.7 - - - -
4537D GLN* 4.1 9.9 - - - -
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Residues in contact with TYR4526 (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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4446D MET* 3.3 28.3 - - + +
4448D GLU* 3.9 19.4 + - + -
4517D TRP* 4.5 2.0 - - - +
4518D PRO* 3.8 6.2 - - - +
4520D TYR* 4.8 1.1 - - + -
4524D GLU 3.9 4.5 - - - +
4525D GLY* 1.3 74.8 - - - +
4527D LEU* 1.3 70.1 + - - +
4528D GLN* 3.2 34.7 + - + -
4535D ALA* 3.4 5.2 - - - +
4536D ALA* 2.9 42.5 + - + +
4537D GLN 3.5 23.1 + - - -
4539D LEU* 3.6 56.9 - - + +
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Residues in contact with LEU4527 (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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4446D MET 3.0 8.5 + - - +
4447D TYR* 3.1 4.9 - - - +
4448D GLU 2.9 24.4 + - - -
4499D PHE* 3.4 36.3 - - + -
4515D PRO* 4.9 2.7 - - + -
4516D HIS 3.8 17.5 - - - +
4517D TRP* 3.4 39.0 - - + +
4526D TYR* 1.3 76.9 - - - +
4528D GLN* 1.3 60.7 + - - +
4529D ILE* 3.5 11.8 + - + -
4533D THR* 3.8 20.4 - - + -
4534D GLN* 3.5 28.0 - - - -
4535D ALA* 3.7 3.6 - - - +
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Residues in contact with GLN4528 (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* 6.1 1.2 - - - +
4448D GLU* 3.5 14.5 + - - +
4450D GLN* 6.2 1.8 - - - +
4526D TYR* 3.2 34.6 + - + -
4527D LEU* 1.3 70.9 - - - +
4529D ILE* 1.3 59.0 + - - +
4532D ASN 3.9 1.9 - - - +
4533D THR* 3.2 8.8 - - - +
4534D GLN* 2.8 69.1 + - - +
4536D ALA* 3.6 18.8 - - + +
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Residues in contact with ILE4529 (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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4447D TYR* 3.9 29.4 - - + -
4448D GLU 2.9 12.0 + - - +
4449D PHE* 3.5 24.9 - - + -
4450D GLN* 2.8 31.0 + - - +
4492D LEU* 3.9 9.2 - - + -
4495D MET* 3.7 21.3 - - + -
4496D VAL* 4.0 8.1 - - + -
4499D PHE* 4.9 3.1 - - + -
4500D TRP* 4.2 22.0 - - + -
4517D TRP* 4.4 2.7 - - + -
4527D LEU* 3.9 29.2 - - + +
4528D GLN* 1.3 74.6 - - - +
4530D GLY* 1.3 61.2 + - - +
4532D ASN 4.7 0.4 - - - -
4533D THR* 3.6 3.8 - - + -
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Residues in contact with GLY4530 (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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4450D GLN* 3.4 15.9 - - - -
4451D TYR* 4.5 5.8 - - - -
4492D LEU* 3.8 19.8 - - - +
4528D GLN 4.0 1.2 + - - -
4529D ILE* 1.3 77.4 - - - +
4531D ALA* 1.3 68.6 + - - +
4532D ASN 3.0 6.7 + - - -
4533D THR* 2.9 17.8 + - - -
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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