Contacts of the helix formed by residues 123 - 131 (chain F) in PDB entry 6D84
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 CYS 123 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F THR 4.0 3.6 - - - -
120F GLU 3.7 18.2 - - - +
121F TYR 3.4 2.4 - - - -
122F LEU* 1.3 78.4 - - - +
124F GLU* 1.3 61.5 + - - +
126F LEU* 3.4 2.9 + - - +
127F ARG* 2.9 22.9 + - - +
148F LEU* 4.6 7.0 - - - -
155F LEU* 3.8 26.9 - - - -
159F GLN* 3.6 46.4 - - + +
161F PHE* 3.2 18.4 - - + -
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Residues in contact with GLU 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F TYR 4.9 0.8 + - - +
123F CYS* 1.3 77.3 - - - +
125F PRO* 1.4 66.5 - - + +
127F ARG* 3.2 33.3 + - - +
128F LYS* 2.9 30.4 + - + +
159F GLN* 5.3 2.0 - - - +
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Residues in contact with PRO 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F VAL* 3.7 32.8 - - + +
95F CYS* 4.5 16.6 - - + -
110F MET* 3.9 22.4 - - + -
121F TYR 4.0 15.9 - - - +
122F LEU 4.5 1.1 - - - -
123F CYS 3.9 0.7 - - - -
124F GLU* 1.4 93.0 - - + +
126F LEU* 1.3 57.4 + - - +
128F LYS* 3.3 9.5 + - + +
129F CYS* 2.9 35.4 + - - -
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Residues in contact with LEU 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F VAL* 3.9 9.0 - - + -
110F MET* 4.7 7.4 - - + +
122F LEU 3.5 12.3 - - - +
123F CYS 3.4 8.9 + - - +
124F GLU 3.2 0.4 - - - -
125F PRO* 1.3 79.5 - - - +
127F ARG* 1.3 57.1 + - - +
129F CYS* 3.3 3.1 + - - -
130F LEU* 2.9 32.6 + - + +
141F ALA* 3.8 25.1 - - + +
144F CYS* 3.7 44.2 - - + +
145F VAL* 4.2 13.9 - - + -
148F LEU* 4.2 15.0 - - + -
161F PHE* 4.0 21.3 - - + -
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Residues in contact with ARG 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F CYS 2.9 13.9 + - - +
124F GLU* 3.4 35.2 + - - +
126F LEU* 1.3 76.7 - - - +
128F LYS* 1.3 61.1 + - - +
130F LEU* 3.3 17.4 - - + +
131F LYS* 3.3 25.4 + - + +
159F GLN* 2.5 55.0 + - - +
160F GLY 4.9 1.0 + - - -
161F PHE* 3.3 22.7 - - + -
164F THR* 4.5 14.7 - - + +
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Residues in contact with LYS 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F CYS* 4.3 18.5 + - + +
96F GLU* 4.9 19.9 - - + +
103F ARG* 5.2 3.4 - - - +
124F GLU* 2.9 17.6 + - + +
125F PRO* 3.6 11.7 - - + +
126F LEU 3.2 0.2 - - - -
127F ARG* 1.3 76.6 - - - +
129F CYS* 1.3 59.7 + - - +
131F LYS* 2.9 23.4 + - + +
132F ASP* 3.2 21.9 + - - +
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Residues in contact with CYS 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F CYS* 3.9 29.2 - - - -
103F ARG* 5.1 4.7 - - - -
107F VAL* 3.7 32.1 - - + -
125F PRO 2.9 19.9 + - - +
126F LEU 3.3 4.2 + - - +
128F LYS* 1.3 76.3 - - - +
130F LEU* 1.3 65.0 + - - +
132F ASP* 3.6 21.2 - - - +
137F VAL* 3.8 27.9 - - + +
138F ARG* 4.0 3.6 - - - -
141F ALA* 3.9 6.9 - - + +
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Residues in contact with LEU 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F LEU* 2.9 20.9 + - + +
127F ARG* 3.3 20.0 - - + +
128F LYS 3.2 0.2 - - - -
129F CYS* 1.3 77.8 - - - +
131F LYS* 1.3 63.8 + - + +
132F ASP 3.2 3.5 + - - -
138F ARG* 3.7 19.4 - - - +
141F ALA* 3.8 30.7 - - + +
142F ALA* 4.1 0.9 - - - +
145F VAL* 3.9 18.8 - - + -
161F PHE* 4.3 9.6 - - + -
164F THR* 3.4 34.5 - - + +
165F LEU* 6.0 1.3 - - + +
168F LEU* 3.8 35.4 - - + +
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Residues in contact with LYS 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F ARG* 3.3 15.2 + - + +
128F LYS* 2.9 14.9 + - + +
130F LEU* 1.3 79.4 - - + +
132F ASP* 1.3 62.9 + - - +
164F THR* 5.2 16.0 - - - +
167F ASP* 4.7 20.6 + - - +
168F LEU* 6.4 0.4 - - - +
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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