Contacts of the strand formed by residues 98 - 102 (chain 3) in PDB entry 5NEU
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 TYR 98 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291 HIS* 2.3 43.2 + - + -
301 THR* 3.4 20.4 - - + -
351 ILE* 3.2 19.4 - - + +
651 LEU* 6.0 3.4 - - + -
443 PHE* 5.6 1.7 - - - +
943 LEU* 3.2 33.7 - - + -
953 ALA 4.2 2.3 + - - +
963 GLN 3.5 3.9 - - - +
973 TYR* 1.3 86.4 - - + +
993 THR* 1.3 66.2 + - - +
1003 GLN 4.5 2.7 - - - +
1703 THR* 3.3 15.8 - - + +
1713 ALA* 5.6 1.7 - - - +
2113 LEU* 3.6 25.6 - - + -
2123 ARG 3.2 29.8 - - - +
2133 LEU 3.8 4.0 - - - -
2143 PRO* 3.6 21.3 - - + -
2153 VAL* 3.9 6.4 - - - +
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Residues in contact with THR 99 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983 TYR* 1.3 77.6 - - - +
1003 GLN* 1.3 68.8 + - - +
1693 TYR* 3.4 16.1 - - - +
1703 THR* 2.8 24.4 + - - +
1713 ALA* 4.1 4.0 + - - +
2123 ARG 3.5 0.2 + - - -
2133 LEU* 3.3 44.7 + - + +
2153 VAL* 3.7 25.8 - - + -
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Residues in contact with GLN 100 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983 TYR* 3.9 1.8 - - - +
993 THR* 1.3 89.3 + - - +
1013 TYR* 1.3 61.2 + - - +
1673 TYR* 4.1 19.4 - - + +
1683 THR 3.2 17.9 - - - +
1693 TYR* 3.5 25.0 + - + -
1703 THR* 3.8 4.2 - - - +
2113 LEU* 3.9 2.1 - - - +
2123 ARG* 3.0 65.4 + - + +
2133 LEU* 3.4 19.3 - - - +
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Residues in contact with TYR 101 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793 LEU* 4.1 13.9 + - - +
803 SER* 5.0 4.4 - - - -
813 LEU* 4.1 16.7 - - + +
1003 GLN* 1.3 74.0 - - - +
1023 SER* 1.3 80.1 + - - +
1033 GLY 4.5 8.1 - - - -
1053 ILE* 4.6 8.7 - - + +
1613 TYR* 4.6 6.0 - + - -
1673 TYR* 3.3 9.7 - - - -
1683 THR* 2.9 66.5 + - - -
1693 TYR 3.9 12.6 - - - -
1703 THR* 3.9 20.4 - - - -
1813 GLN* 3.9 21.0 + - - +
2093 PHE* 3.5 28.7 - + + -
2103 GLU 3.7 13.0 - - - +
2113 LEU* 4.3 17.3 - - + +
2123 ARG* 5.2 0.4 - - - -
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Residues in contact with SER 102 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013 TYR* 1.3 86.1 - - - +
1033 GLY* 1.3 61.2 + - - +
1613 TYR* 3.8 15.0 - - - -
1663 ASP 3.7 10.8 - - - -
1673 TYR* 3.4 27.2 - - - -
2083 ASP 3.8 3.3 + - - +
2093 PHE* 3.4 6.8 - - - -
2103 GLU* 3.1 34.4 + - - +
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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