Contacts of the strand formed by residues 5444 - 5450 (chain E) 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 THR5444 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5346E TYR* 3.4 10.8 - - + +
5348E VAL* 5.4 2.2 - - + -
5434E ALA* 3.6 37.5 - - + +
5437E HIS* 3.0 19.5 - - + -
5438E ARG* 3.3 11.4 + - - -
5442E ALA 3.0 15.5 + - - -
5443E PRO* 1.3 70.5 - - - +
5445E TYR* 1.3 64.3 + - - +
5519E GLU* 3.3 14.0 - - - +
5520E TYR* 2.7 49.7 + - + -
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Residues in contact with TYR5445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5346E TYR 3.1 9.3 + - - +
5347E MET* 3.4 10.0 - - + -
5348E VAL* 2.8 27.0 + - - +
5443E PRO* 4.4 11.2 - - + +
5444E THR* 1.3 81.2 - - - +
5446E MET* 1.3 65.5 + - - +
5503E PHE* 3.9 17.0 - + - -
5507E GLY 3.5 20.0 + - - -
5508E ASN* 3.2 29.2 + - - +
5509E PRO* 3.6 22.4 - - + -
5510E ASN* 4.5 0.9 - - - -
5517E TRP* 3.8 34.8 - + + +
5518E PRO 3.7 14.6 - - - -
5519E GLU* 3.6 30.9 - - + +
5520E TYR* 4.0 3.6 - - - +
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Residues in contact with MET5446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5348E VAL* 3.0 25.6 - - + +
5349E GLY* 5.2 2.0 - - - -
5350E ILE* 5.5 1.6 - - + -
5430E SER* 3.8 28.3 - - - +
5431E VAL* 3.9 14.8 - - + +
5434E ALA* 3.4 25.6 - - + -
5445E TYR* 1.3 79.1 - - - +
5447E TYR* 1.3 60.9 + - - +
5517E TRP* 3.0 14.4 + - - +
5520E TYR* 3.7 33.2 - - + +
5525E GLY 4.8 1.2 + - - -
5526E TYR* 3.4 18.3 - - + +
5527E LEU 3.0 20.8 + - - -
5539E LEU* 3.8 24.7 - - + -
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Residues in contact with TYR5447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5244E ILE* 5.1 0.2 - - + -
5245E SER 4.9 0.7 - - - -
5246E GLU* 3.1 39.4 - - + +
5247E SER* 4.6 0.3 + - - -
5347E MET* 4.1 12.6 - - + -
5348E VAL 3.3 2.5 + - - +
5349E GLY* 3.3 28.5 - - - -
5350E ILE* 3.1 36.0 + - - +
5351E ASN* 4.4 2.1 + - - -
5446E MET* 1.3 75.2 - - - +
5448E GLU* 1.3 63.7 + - - +
5449E PHE* 3.7 20.6 - + + -
5471E GLU* 4.2 9.3 - - + +
5500E TRP* 3.7 30.0 - + - -
5517E TRP* 3.6 20.2 - + + -
5526E TYR* 4.5 4.3 - - - -
5527E LEU 3.0 15.3 - - - +
5529E ILE* 3.8 19.5 - - + -
5539E LEU* 4.3 5.1 - - - +
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Residues in contact with GLU5448 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5350E ILE* 3.1 19.0 - - + +
5352E LYS* 3.4 48.7 + - + +
5447E TYR* 1.3 76.2 - - - +
5449E PHE* 1.3 63.8 - - - +
5450E GLN* 3.7 3.6 + - + +
5526E TYR* 3.8 23.2 + - + -
5527E LEU 3.0 5.7 + - - -
5528E GLN* 3.6 10.8 + - + +
5529E ILE 3.0 22.5 + - - +
5539E LEU* 3.6 24.7 - - + +
5540E LYS* 4.3 15.2 + - - -
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Residues in contact with PHE5449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5350E ILE 2.7 9.8 + - - +
5351E ASN* 3.1 22.9 - - - +
5352E LYS* 2.8 28.0 + - - +
5447E TYR* 3.7 11.6 - + + -
5448E GLU* 1.3 71.6 - - - +
5450E GLN* 1.3 59.0 + - - +
5451E TYR* 3.7 39.3 - + + -
5466E GLY* 3.9 2.1 - - - -
5470E ASP* 3.6 13.5 - - + -
5471E GLU* 3.6 43.7 - - + -
5474E SER* 3.8 24.7 - - - -
5492E LEU* 4.1 7.9 - - + -
5496E VAL* 4.7 3.4 - - + -
5500E TRP* 6.4 0.7 - + - -
5529E ILE* 3.6 33.2 - - + -
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Residues in contact with GLN5450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5352E LYS* 3.6 49.4 + - + +
5448E GLU* 3.7 3.4 + - + +
5449E PHE* 1.3 74.2 - - - +
5451E TYR* 1.3 64.4 + - - +
5465E ILE* 4.0 20.2 - - + +
5466E GLY* 4.4 1.3 - - - -
5528E GLN* 6.1 0.7 - - - +
5529E ILE 2.8 13.6 + - - +
5530E GLY* 3.6 13.8 - - - -
5531E ALA 4.4 1.4 + - - -
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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