Contacts of the strand formed by residues 273 - 277 (chain 5) in PDB entry 5U8T
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 ASN 273 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1675 ILE* 5.5 7.5 - - + +
2575 LYS* 3.7 33.3 - - + +
2585 LEU 3.1 17.3 - - - +
2595 GLN* 4.4 6.5 - - + -
2715 PRO 5.1 1.8 - - - +
2725 ARG* 1.3 75.7 - - - +
2745 LEU* 1.3 70.8 + - - +
2755 THR* 4.1 5.1 + - - -
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Residues in contact with LEU 274 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1485 LEU* 3.8 32.7 - - + +
1515 LEU 5.4 0.2 - - - +
2575 LYS* 5.4 0.4 - - - -
2585 LEU* 2.9 36.8 + - + +
2725 ARG* 4.2 10.2 - - + -
2735 ASN* 1.3 83.8 - - - +
2755 THR* 1.3 63.4 + - - +
2765 MET* 4.0 14.9 - - + +
2985 TYR* 3.6 35.2 - - + +
3265 PRO* 4.8 27.1 - - + +
3275 TYR* 5.7 2.2 - - - +
3285 ILE* 6.0 0.4 - - + -
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Residues in contact with THR 275 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2555 PHE* 4.8 17.3 - - + +
2565 LEU 3.3 19.7 - - - +
2575 LYS* 4.8 15.3 - - + +
2735 ASN* 4.7 4.3 + - - -
2745 LEU* 1.3 71.9 - - - +
2765 MET* 1.3 69.2 + - - +
2775 THR* 5.2 1.6 - - + -
3015 TYR* 6.0 1.6 - - - +
3265 PRO 4.8 7.2 + - - -
3275 TYR* 3.1 19.4 - - + +
3285 ILE 3.1 20.3 + - - -
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Residues in contact with MET 276 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1485 LEU* 5.5 2.5 - - + -
1515 LEU* 6.4 0.2 - - + -
1625 LEU* 4.6 15.7 - - + -
2555 PHE* 3.4 0.9 - - - -
2565 LEU* 2.8 29.7 + - + +
2585 LEU* 3.5 43.1 - - + -
2745 LEU* 3.8 20.6 + - + +
2755 THR* 1.3 77.7 - - - +
2775 THR* 1.3 69.3 - - - +
2945 ILE* 4.3 15.7 - - - -
3275 TYR* 5.2 1.1 - - - -
3285 ILE* 3.1 54.5 - - + +
3305 ILE* 3.6 15.9 - - + -
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Residues in contact with THR 277 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3143 LEU* 3.5 13.4 - - + +
2535 GLN* 3.1 30.8 + - - +
2555 PHE* 3.5 33.7 - - + +
2565 LEU* 3.9 1.3 - - - -
2755 THR* 5.2 1.8 - - + -
2765 MET* 1.3 83.8 - - - +
2785 CYS* 1.3 52.8 + - - +
3275 TYR* 4.7 3.3 - - + -
3285 ILE 3.3 4.9 + - - -
3295 LYS* 2.4 54.4 + - - +
3305 ILE* 3.2 12.8 - - - +
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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