Contacts of the strand formed by residues 110 - 112 (chain A) in PDB entry 3KG2
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 VAL 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A TYR* 4.8 2.7 - - + +
85A ILE* 5.3 1.6 - - + -
86A THR* 4.4 24.5 - - + +
89A CYS* 4.8 2.9 - - + -
96A PHE* 3.4 19.7 - - + +
98A THR* 4.6 8.5 - - + -
103A THR* 4.5 9.4 - - + -
107A HIS* 3.6 16.8 - - + +
108A PRO 3.2 11.5 - - - +
109A PHE* 1.3 85.3 - - - +
111A ILE* 1.3 68.6 + - - +
112A GLN* 3.9 28.7 + - + +
330A GLU* 5.7 0.2 - - - +
350A ASN 3.5 18.1 + - - +
351A GLY* 3.6 8.7 - - - -
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER* 5.5 0.9 - - - -
96A PHE 2.7 11.9 + - - +
97A ILE* 3.3 23.7 - - + +
98A THR* 2.8 29.6 + - - +
109A PHE 5.5 0.7 - - - -
110A VAL* 1.3 82.2 - - - +
112A GLN* 1.3 61.5 + - - +
113A MET* 3.6 12.9 + - + -
291A VAL* 5.0 5.8 - - + -
330A GLU* 5.1 8.1 - - + +
333A LEU* 3.8 34.3 - - + -
334A LYS* 4.3 17.7 - - + +
347A PHE* 3.5 31.4 - - + -
350A ASN 5.3 0.9 - - - +
351A GLY* 4.4 11.0 - - - -
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Residues in contact with GLN 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 4.3 9.0 - - - +
98A THR* 3.4 8.1 - - + +
100A SER 5.0 2.7 - - - +
101A PHE 5.1 0.2 - - - +
102A PRO* 3.3 26.4 - - + +
103A THR* 2.7 45.2 + - - +
107A HIS 5.6 0.7 - - - +
110A VAL* 3.9 17.9 - - + +
111A ILE* 1.3 74.8 - - - +
113A MET* 1.3 64.1 + - - +
114A ARG 3.4 9.8 + - - +
347A PHE* 3.8 2.3 - - - -
351A GLY* 3.4 20.1 + - - +
352A LYS* 4.1 22.6 - - - +
353A ARG* 3.2 23.4 + - - +
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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
------------------------------------------------------------
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