Contacts of the helix formed by residues 124 - 129 (chain A) in PDB entry 3KK3
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 PHE 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.3 39.0 - - + +
11A LYS* 3.9 11.7 - - - -
12A LEU* 3.7 20.6 - - + -
80A LEU* 3.4 37.2 - - + -
84A THR* 3.5 10.1 - - - -
120A LEU* 4.3 17.7 - - + -
121A ASP* 3.1 22.1 + - + +
123A ASP* 1.3 77.7 - - - +
125A ARG* 1.3 66.7 + - - +
126A LYS 2.9 4.6 + - - -
127A TYR* 3.1 29.7 + + + +
128A THR* 4.4 4.6 + - + -
153A TRP* 3.7 18.4 - + - -
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Residues in contact with ARG 125 (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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7A THR* 4.7 1.6 - - - +
119A PRO* 4.7 8.3 - - - +
120A LEU* 3.0 38.5 + - + +
121A ASP 3.1 7.4 + - - +
122A GLU* 3.1 54.5 + - - +
124A PHE* 1.3 77.2 - - - +
126A LYS* 1.3 57.5 + - - +
128A THR* 2.5 28.5 + - - -
145A GLN* 3.8 21.8 - - - +
146A TYR 2.5 27.8 - - - +
147A ASN* 3.1 40.1 + - - +
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Residues in contact with LYS 126 (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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54A ASN* 3.1 34.9 + - - +
55A PRO* 6.2 0.7 - - + -
56A TYR* 3.6 18.9 - - + -
122A GLU 4.5 1.6 + - - +
123A ASP* 3.1 30.0 + - - +
124A PHE 2.9 1.4 + - - +
125A ARG* 1.3 75.0 - - - +
127A TYR* 1.3 85.4 + - + +
128A THR 3.1 6.6 + - - -
129A ALA* 3.4 7.4 + - - +
145A GLN* 3.5 15.5 - - - +
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Residues in contact with TYR 127 (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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11A LYS* 6.3 0.2 - - - -
12A LEU* 3.4 31.9 - - + +
17A ASP* 3.9 3.8 + - - -
18A GLY* 3.7 17.3 - - - -
19A PRO* 3.4 26.2 - - + +
56A TYR* 3.7 34.3 + + - +
58A THR* 4.6 1.0 - - - +
80A LEU* 3.1 28.3 - - + +
123A ASP 4.1 13.8 + - - -
124A PHE* 3.1 45.1 + + + +
126A LYS* 1.3 94.0 - - + +
128A THR* 1.3 57.4 + - - +
129A ALA 3.2 2.9 + - - +
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Residues in contact with THR 128 (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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58A THR* 4.2 4.2 - - - +
77A PHE* 4.0 15.4 - - + -
80A LEU* 4.0 13.0 - - + -
120A LEU* 3.9 23.6 - - + -
124A PHE* 4.6 8.1 - - + +
125A ARG 2.5 23.4 + - - +
127A TYR* 1.3 80.1 - - - +
129A ALA* 1.3 66.6 + - - +
130A PHE* 3.2 17.5 + - - +
144A TYR 4.0 0.8 - - - +
145A GLN* 4.4 0.6 - - - -
146A TYR* 2.9 33.6 + - - +
150A PRO* 4.1 12.8 - - + -
153A TRP* 5.9 1.8 - - + -
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Residues in contact with ALA 129 (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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50A ILE* 3.5 20.2 - - + -
54A ASN* 3.4 26.2 - - - +
56A TYR 3.5 16.8 - - - +
57A ASN* 3.1 4.3 - - - -
58A THR* 2.9 25.5 + - - +
126A LYS 3.4 5.6 + - - +
127A TYR 3.2 3.3 - - - +
128A THR* 1.3 79.0 + - - +
130A PHE* 1.3 59.8 + - - +
143A ARG* 3.8 2.0 - - - +
144A TYR 3.2 9.2 - - - -
145A GLN* 4.3 2.4 - - - +
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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