Contacts of the helix formed by residues 124 - 129 (chain B) in PDB entry 6UJX
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 4.0 21.8 - - + +
11B LYS 4.4 12.6 - - - -
12B LEU* 3.8 22.4 - - + -
80B LEU* 4.2 15.9 - - + -
84B THR* 3.9 8.7 - - + -
120B LEU* 3.8 13.5 - - + -
121B ASP* 2.8 23.9 + - + +
123B ASP* 1.3 79.6 - - - +
125B ARG* 1.3 65.3 + - - +
126B LYS 3.1 2.9 - - - -
127B TYR* 2.8 35.1 + + + +
128B THR* 4.1 14.1 + - + +
153B TRP* 3.1 50.9 - + - -
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B THR* 5.3 1.8 - - - +
119B PRO* 4.5 7.7 - - - +
120B LEU* 2.7 45.0 + - + +
121B ASP 3.4 2.5 - - - +
122B GLU* 3.4 39.6 + - - +
123B ASP 3.4 0.6 - - - -
124B PHE* 1.3 76.3 - - - +
126B LYS* 1.3 57.7 + - - +
128B THR* 2.9 31.4 + - - -
145B GLN* 3.2 21.8 - - - +
146B TYR 3.5 17.7 - - - +
147B ASN* 3.0 50.0 + - - +
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Residues in contact with LYS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ASN* 3.0 31.9 + - + +
55B PRO* 6.0 0.4 - - + -
56B TYR* 3.7 26.7 - - + +
122B GLU 4.7 1.4 + - - -
123B ASP* 3.2 42.0 + - - +
124B PHE 4.1 0.7 - - - +
125B ARG* 1.3 78.3 - - - +
127B TYR* 1.3 80.7 + - + +
128B THR 3.1 1.0 + - - -
129B ALA 3.5 5.9 + - - -
145B GLN* 3.1 18.1 + - - +
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 4.2 21.3 - - + +
17B ASP* 4.5 1.3 + - - -
18B GLY* 3.9 17.7 - - - -
19B PRO* 3.7 23.7 - - + +
56B TYR* 3.3 51.0 + + - +
57B ASN 6.1 0.2 - - - -
58B THR* 4.5 2.1 + - - -
80B LEU* 3.9 21.8 - - + +
123B ASP 4.0 13.4 + - - -
124B PHE* 2.8 46.9 + + + +
126B LYS* 1.3 89.2 + - + +
128B THR* 1.3 59.4 + - + +
129B ALA 3.5 1.0 + - - +
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Residues in contact with THR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PHE* 4.2 22.9 - - - -
80B LEU* 4.2 15.3 - - + -
120B LEU* 5.1 3.6 - - + -
124B PHE* 4.2 20.0 - - + +
125B ARG* 2.9 21.9 + - - +
127B TYR* 1.3 80.8 - - - +
129B ALA* 1.3 66.5 + - - +
130B PHE* 3.6 13.7 + - - +
144B TYR 4.6 0.3 - - - +
146B TYR* 3.1 34.4 + - + +
150B PRO* 4.6 14.6 - - + -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ILE* 3.4 26.9 - - + -
54B ASN* 3.7 12.3 - - - +
56B TYR* 3.5 22.2 - - - +
57B ASN* 3.6 3.6 - - - -
58B THR* 3.1 24.8 + - - -
125B ARG 4.1 1.6 + - - -
126B LYS 3.5 4.0 + - - +
127B TYR 3.5 1.8 - - - +
128B THR* 1.3 81.0 + - - +
130B PHE* 1.3 59.2 + - - +
143B ARG* 3.9 5.4 - - - +
144B TYR 3.2 8.7 - - - -
145B GLN* 4.4 1.3 - - - +
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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