Contacts of the helix formed by residues 116 - 121 (chain B) in PDB entry 5XTD
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 LEU 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B CYS* 3.0 18.0 + - + +
115B LYS* 1.3 76.4 - - - +
117B CYS* 1.3 67.0 + - - +
118B GLU 3.0 1.8 - - - -
119B ALA* 2.7 27.2 + - - +
120B ILE* 3.0 21.9 + - + +
159B ALA* 3.2 40.6 - - + +
161B PRO* 3.8 21.8 - - + -
129M PRO* 5.9 0.4 - - + -
243M TRP* 4.4 1.3 - - + -
381Q HIS* 5.1 7.4 - - + -
382Q PHE* 4.1 28.5 - - + -
385Q TYR* 4.5 6.5 - - + +
386Q THR* 3.9 20.6 - - + -
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Residues in contact with CYS 117 (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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116B LEU* 1.3 84.4 - - - +
118B GLU* 1.3 58.1 + - - +
120B ILE* 3.9 4.3 - - - +
121B CYS* 3.4 16.5 + - - +
126B ILE* 3.3 20.0 - - + +
156B CYS* 3.6 27.6 - - + -
159B ALA* 4.1 3.8 - - - -
160B CYS* 3.8 25.6 - - - -
165B ILE* 5.1 0.2 - - + -
301B SF4 3.1 51.3 - - - -
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Residues in contact with GLU 118 (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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115B LYS* 3.1 27.2 + - - +
116B LEU 3.0 0.2 - - - -
117B CYS* 1.3 81.6 - - - +
119B ALA* 1.3 57.0 + - - +
120B ILE 3.2 2.0 + - - -
121B CYS* 4.5 7.5 + - - +
124B GLN* 5.3 5.2 - - - +
126B ILE* 4.1 20.8 - - + +
127B THR* 5.1 0.3 - - - +
128B ILE* 3.3 38.9 + - + +
301B SF4 4.6 0.6 - - - -
244M GLU* 3.0 31.4 - - - +
266M ARG* 5.3 3.3 + - - -
231P ARG* 3.3 28.2 + - - +
233P PHE* 3.5 19.1 - - + -
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Residues in contact with ALA 119 (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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115B LYS 3.9 0.6 + - - -
116B LEU* 2.7 28.4 + - - +
118B GLU* 1.3 72.9 - - - +
120B ILE* 1.3 58.6 + - - +
121B CYS 5.4 0.2 - - - -
243M TRP* 4.0 19.3 - - + +
233P PHE* 3.4 27.3 - - + -
235P LEU* 5.7 2.3 - - + +
128Q THR* 5.9 1.6 - - - +
131Q GLN* 3.5 15.1 + - - -
385Q TYR 4.3 9.6 - - - +
386Q THR* 4.6 14.8 - - - +
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Residues in contact with ILE 120 (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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116B LEU* 3.0 11.8 + - + +
117B CYS* 3.6 4.9 + - - +
118B GLU 3.2 0.2 - - - -
119B ALA* 1.3 80.7 - - - +
121B CYS* 1.3 71.9 + - - +
122B PRO* 2.7 12.1 - - - +
155B PHE* 3.5 39.1 - - + -
156B CYS* 5.2 1.8 - - - -
159B ALA* 3.4 18.4 - - + -
130Q LEU* 6.0 4.9 - - + -
131Q GLN* 3.4 14.5 + - + +
385Q TYR* 3.1 61.7 - - + +
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Residues in contact with CYS 121 (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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117B CYS 3.4 14.4 + - - +
118B GLU 4.5 3.5 + - - +
119B ALA 5.4 0.2 - - - -
120B ILE* 1.3 73.6 - - - +
122B PRO* 1.3 64.1 - - - +
123B ALA* 4.0 2.9 - - - -
124B GLN* 2.6 38.9 + - - +
125B ALA* 3.0 35.7 - - - +
126B ILE* 4.0 8.5 - - + +
156B CYS* 4.5 0.8 - - - -
302B SF4 2.9 46.4 - - - -
131Q GLN* 4.6 1.9 + - - -
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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