Contacts of the helix formed by residues 124 - 134 (chain B) in PDB entry 7CE1
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 MET 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B LYS 4.1 4.0 + - - +
123B SER* 1.3 78.4 - - - +
125B VAL* 1.3 66.0 + - - +
126B PRO* 3.2 2.7 - - - -
127B ILE* 3.2 29.0 + - + -
128B ARG* 3.5 42.9 + - + +
149B PRO* 3.9 42.4 - - + +
150B ARG* 3.7 13.0 - - + -
153B PHE* 4.3 13.9 - - + -
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Residues in contact with VAL 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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117B HIS* 5.4 0.7 - - + -
121B LYS 4.8 1.8 - - - +
122B ASP* 3.6 30.5 - - + +
124B MET* 1.3 78.4 - - - +
126B PRO* 1.3 72.3 - - + +
128B ARG* 3.7 17.4 + - - +
129B TYR* 3.5 16.4 + - + +
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Residues in contact with PRO 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL* 3.9 17.7 - - + -
115B THR* 3.7 25.8 - - + +
116B PRO 4.7 5.4 - - - +
117B HIS* 3.9 15.7 - - + -
122B ASP 3.5 11.2 - - - +
123B SER 4.0 3.4 - - - +
124B MET 3.4 0.9 - - - -
125B VAL* 1.3 99.0 - - + +
127B ILE* 1.3 77.2 + - + +
129B TYR* 3.0 19.1 + - + +
130B ILE* 3.1 18.9 - - + +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL* 4.1 19.7 - - + -
123B SER 3.6 13.9 - - - +
124B MET* 3.2 14.5 + - + +
126B PRO* 1.3 88.8 - - + +
128B ARG* 1.3 60.9 + - - +
130B ILE* 3.3 9.7 + - - +
131B LEU* 3.1 28.3 + - + +
139B VAL* 6.1 0.2 - - - -
141B ILE* 4.5 2.7 - - + -
150B ARG* 3.6 34.3 - - + -
153B PHE* 3.8 25.6 - - + -
154B MET* 3.4 39.0 - - + -
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Residues in contact with ARG 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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124B MET* 3.5 45.8 + - + +
125B VAL* 4.6 13.4 + - - +
126B PRO 3.3 0.2 - - - -
127B ILE* 1.3 73.5 - - - +
129B TYR* 1.3 58.0 + - - +
131B LEU* 3.0 3.2 + - + +
132B GLU* 2.4 63.5 + - + +
153B PHE* 3.3 37.0 - - + -
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Residues in contact with TYR 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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64A GLN* 4.7 20.2 - - + -
67A ARG* 4.7 6.1 + - - -
109A GLN* 5.5 6.4 + - - -
111A HIS* 2.7 42.7 + + - -
115B THR* 5.0 8.3 - - + -
125B VAL* 3.5 12.4 + - + +
126B PRO* 3.0 14.4 + - + +
128B ARG* 1.3 75.6 - - - +
130B ILE* 1.3 75.6 + - + +
132B GLU* 4.1 10.2 - - - +
133B THR* 2.8 50.5 + - - +
135B SER* 3.9 7.9 - - - -
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Residues in contact with ILE 130 (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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81B ALA* 4.0 19.3 - - + -
83B VAL* 5.0 5.8 - - + -
115B THR* 3.9 31.4 - - + +
126B PRO* 3.1 28.3 + - + +
127B ILE* 3.5 9.4 - - - +
128B ARG 3.1 1.0 - - - -
129B TYR* 1.3 84.3 - - + +
131B LEU* 1.3 59.8 + - + +
134B GLY* 2.6 33.5 + - - -
135B SER* 3.2 18.5 + - - +
136B ALA* 3.6 31.6 - - + +
139B VAL* 3.9 18.4 - - + -
159B MET* 4.7 4.3 - - + -
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Residues in contact with LEU 131 (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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127B ILE* 3.1 33.7 - - + +
128B ARG* 3.0 9.5 + - + +
130B ILE* 1.3 81.3 - - + +
132B GLU* 1.3 65.8 + - + +
133B THR 3.0 2.9 + - - -
134B GLY* 3.3 10.8 + - - +
153B PHE* 4.5 13.5 - - + -
154B MET* 4.4 10.3 - - + -
157B ARG* 4.1 34.3 + - + +
159B MET* 3.6 45.1 - - + -
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Residues in contact with GLU 132 (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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19A ARG* 3.9 20.6 + - - +
64A GLN* 5.2 5.5 - - - +
128B ARG* 2.4 55.1 + - + +
129B TYR* 3.8 10.5 - - + +
131B LEU* 1.3 74.4 - - + +
133B THR* 1.3 58.8 + - - +
157B ARG* 5.7 7.9 - - - +
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Residues in contact with THR 133 (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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19A ARG* 2.5 46.2 + - - +
64A GLN* 4.9 10.1 + - + +
65A PRO 5.9 0.2 - - - +
67A ARG* 4.8 11.0 - - + -
71B ARG* 5.4 0.4 - - - +
129B TYR* 2.8 46.3 + - - +
131B LEU 4.0 0.2 - - - -
132B GLU* 1.3 81.4 - - - +
134B GLY* 1.3 60.5 + - - +
135B SER* 3.4 24.9 - - - -
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Residues in contact with GLY 134 (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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71B ARG* 4.2 2.6 + - - -
77B THR* 3.5 18.1 - - - +
130B ILE 2.6 16.2 + - - -
131B LEU* 3.3 10.5 + - - -
133B THR* 1.3 76.4 - - - +
135B SER* 1.3 55.0 + - - -
136B ALA 3.4 8.3 - - - -
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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