Contacts of the strand formed by residues 13 - 17 (chain 2) in PDB entry 4UOW
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 ASP 13 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112 PRO* 4.4 0.2 - - - +
122 SER* 1.3 90.4 - - - +
142 ILE* 1.3 70.4 + - - +
152 SER* 5.9 0.2 - - - +
932 ASN* 3.3 20.5 + - - +
952 HIS* 2.9 29.1 + - + +
443 GLU* 3.9 4.9 - - - +
473 GLN* 2.9 37.3 + - - +
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Residues in contact with ILE 14 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112 PRO* 3.6 21.5 - - + -
132 ASP* 1.3 80.1 - - - +
152 SER* 1.3 63.9 + - - +
222 LEU* 3.8 22.0 - - + -
242 VAL* 3.5 31.2 - - + -
922 VAL* 3.7 13.7 - - + -
932 ASN 2.9 9.1 + - - +
942 ILE* 3.4 22.8 - - + -
952 HIS* 2.9 25.2 + - - -
443 GLU* 5.6 0.2 - - - +
813 VAL* 5.2 0.4 - - + -
923 PHE* 3.5 37.0 - - + -
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Residues in contact with SER 15 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132 ASP* 5.9 0.2 - - - +
142 ILE* 1.3 77.5 + - - +
162 ILE* 1.3 58.2 + - - +
952 HIS* 3.3 27.6 - - - +
972 ARG* 3.2 31.4 + - - -
833 ARG* 5.5 0.2 - - - -
903 GLU* 2.7 27.4 - - - +
923 PHE* 3.8 5.9 - - - -
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Residues in contact with ILE 16 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152 SER* 1.3 77.0 - - - +
172 ASP* 1.3 71.9 + - - +
202 LYS* 3.9 14.6 - - + +
212 VAL 3.2 34.5 - - - +
222 LEU* 3.7 30.1 - - + -
692 VAL* 3.8 23.1 - - + -
942 ILE* 4.6 1.6 - - + -
952 HIS 3.0 12.0 + - - +
962 ILE* 3.4 9.5 - - + -
972 ARG* 3.0 26.3 + - - +
903 GLU* 3.6 31.4 - - + +
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Residues in contact with ASP 17 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60 LYS* 4.9 6.1 - - - -
981 GLN* 4.6 2.8 - - - +
162 ILE* 1.3 85.0 - - - +
182 GLU* 1.3 66.4 + - - +
192 GLY 3.5 0.3 + - - -
202 LYS* 2.9 30.7 + - + +
692 VAL* 4.2 4.2 - - - +
962 ILE* 4.5 1.3 - - - -
972 ARG* 2.8 42.0 + - - +
982 SER 4.1 13.5 - - - +
853 ARG* 2.9 25.3 + - - -
903 GLU* 3.6 0.2 - - - +
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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
------------------------------------------------------------
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