Contacts of the helix formed by residues 104 - 110 (chain A) in PDB entry 4KLZ
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 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 5.4 1.2 - - - +
30A GLY 5.0 6.9 - - - +
32A VAL* 5.0 1.7 - - - +
101A SER* 3.1 14.2 + - - +
102A ILE 3.3 0.8 - - - -
103A THR* 1.4 87.8 - - - +
105A ARG* 1.4 62.6 + - - +
106A ARG* 3.2 20.7 + - - +
107A SER* 2.8 47.0 + - - +
108A PHE* 3.4 4.3 + - - +
143A GLN* 3.7 3.3 - - - +
144A VAL* 4.1 1.6 - - - -
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Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ASP* 1.4 69.4 + - - +
106A ARG* 1.3 61.3 + - + +
108A PHE* 3.2 5.2 + - - +
109A HIS* 2.8 64.3 + - + +
143A GLN* 2.9 59.3 + - + +
144A VAL* 3.6 17.3 - - + +
148A GLU* 2.2 42.8 + - - -
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ASP* 3.2 11.8 + - - +
105A ARG* 1.3 78.5 - - + +
107A SER* 1.3 57.7 + - - +
109A HIS* 3.4 13.0 + - + +
110A GLU* 2.9 31.5 + - - +
143A GLN* 5.1 0.2 + - - -
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 3.8 20.5 + - - +
32A VAL* 3.6 22.9 - - - -
99A CYS 4.8 1.6 - - - +
100A TYR* 3.6 4.8 - - - +
101A SER 3.0 24.9 + - - -
104A ASP* 2.8 36.1 + - - +
106A ARG* 1.3 76.8 - - - +
108A PHE* 1.3 59.0 + - - -
110A GLU* 3.3 4.9 + - - +
111A VAL* 3.3 20.8 + - - +
114A PHE* 5.6 0.3 - - - -
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Residues in contact with PHE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TYR* 3.5 51.6 - + + -
104A ASP 3.4 6.5 + - - +
105A ARG* 3.2 9.4 + - - +
106A ARG 3.2 0.4 - - - -
107A SER* 1.3 74.6 + - - +
109A HIS* 1.3 87.9 + + - +
111A VAL* 2.9 23.4 + - - +
112A ARG* 5.9 4.9 - - - -
131A LEU* 4.9 0.2 - - + -
144A VAL* 3.9 22.4 - - + -
148A GLU* 3.6 41.1 - - + -
149A GLY* 3.9 10.8 - - - -
152A LEU* 3.7 28.4 - - + +
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Residues in contact with HIS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ARG* 2.8 62.3 + - + +
106A ARG* 3.9 13.5 - - + +
108A PHE* 1.3 86.5 - + - +
110A GLU* 1.3 62.8 + - - +
111A VAL 2.9 1.7 + - - -
112A ARG* 3.0 35.3 + - - +
113A GLU 4.1 0.9 + - - -
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 3.1 24.4 - - + +
106A ARG 2.9 19.2 + - - +
107A SER 3.5 8.1 - - - +
108A PHE 3.1 0.6 - - - -
109A HIS* 1.3 75.1 - - - +
111A VAL* 1.3 63.1 + - - +
112A ARG 3.0 0.4 - - - -
113A GLU* 3.1 21.1 + - + +
114A PHE* 3.0 38.6 + - + -
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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