Contacts of the strand formed by residues 274 - 279 (chain 3) 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 ILE 274 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1683 PRO* 4.7 23.3 - - + +
1713 LEU* 5.0 10.1 - - + -
1823 VAL* 5.5 4.5 - - + -
2563 ILE 3.9 0.3 - - - +
2573 THR* 3.2 5.1 - - - -
2583 VAL* 2.9 30.8 + - + +
2723 ARG* 4.0 7.4 + - + +
2733 SER* 1.3 79.5 - - - +
2753 ASP* 1.3 82.5 + - - +
2763 VAL* 3.9 5.6 + - + +
2983 PHE* 4.8 10.8 - - + -
3193 THR 5.3 5.2 - - - +
3203 LEU* 5.2 0.4 - - - -
3213 ILE* 4.0 26.7 - - + -
1715 VAL* 6.2 3.6 - - + -
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Residues in contact with ASP 275 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2553 ARG* 3.2 41.4 + - + -
2563 ILE 4.4 0.9 - - - -
2573 THR* 3.4 28.7 - - + +
2733 SER 5.0 0.2 - - - +
2743 ILE* 1.3 84.9 - - - +
2763 VAL* 1.3 65.3 + - - +
3193 THR 4.6 6.6 + - - +
3203 LEU* 3.1 32.9 - - + +
4503 ARG* 5.1 3.3 + - - -
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Residues in contact with VAL 276 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1823 VAL* 6.4 0.9 - - + -
2553 ARG* 4.4 0.9 - - - -
2563 ILE* 2.9 32.8 + - + +
2583 VAL* 5.8 3.6 - - + -
2743 ILE* 4.3 8.3 - - + +
2753 ASP* 1.3 80.6 - - - +
2773 ILE* 1.3 64.3 - - - +
2783 LEU* 3.4 23.2 - - + +
2943 VAL* 3.5 35.7 - - + -
3203 LEU* 4.4 0.4 - - - -
3213 ILE* 3.1 43.5 - - + +
3233 GLY 4.1 6.1 - - - +
3263 VAL* 5.4 0.2 - - + -
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Residues in contact with ILE 277 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2183 THR* 3.6 27.4 - - + -
2533 HIS* 3.1 42.8 - - + +
2543 GLN 3.2 7.0 - - - +
2553 ARG* 4.2 6.3 - - + -
2763 VAL* 1.3 72.1 - - - +
2783 LEU* 1.3 62.5 + - - +
2793 ASP* 3.9 12.1 + - - +
3203 LEU* 3.5 39.2 - - + +
3213 ILE 2.9 9.4 + - - +
3223 LEU* 3.5 20.2 - - + -
3233 GLY 3.0 26.3 + - - +
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Residues in contact with LEU 278 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2533 HIS* 3.5 4.2 - - - -
2543 GLN* 2.9 40.0 + - + +
2563 ILE* 3.5 32.8 - - + -
2763 VAL* 3.4 30.5 - - + +
2773 ILE* 1.3 77.2 - - - +
2793 ASP* 1.3 62.0 + - - +
2823 LEU* 3.5 37.5 - - + +
2833 VAL* 3.6 13.9 - - + +
2843 ASP 5.8 0.2 - - - +
2863 THR* 4.7 10.8 - - - +
2943 VAL* 5.6 1.8 - - + -
3263 VAL* 4.3 21.8 - - + -
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Residues in contact with ASP 279 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953 ARG* 3.9 2.4 + - - -
1543 LYS* 4.9 9.9 - - - +
1953 LYS* 5.1 3.0 + - - +
2183 THR* 4.2 12.6 + - - +
2193 THR* 4.9 6.2 + - - -
2513 ILE* 4.4 8.5 - - + +
2523 ASP 3.6 3.5 - - - +
2533 HIS* 3.3 33.9 - - - +
2773 ILE* 3.9 14.0 + - - +
2783 LEU* 1.3 74.8 - - - +
2803 ASP* 1.3 73.4 + - + +
2813 ASP* 3.1 3.3 + - - +
2823 LEU* 3.3 23.6 + - + +
3223 LEU* 4.3 4.3 - - - +
3233 GLY* 6.0 2.2 - - - +
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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