Contacts of the helix formed by residues 123 - 133 (chain B) in PDB entry 3CJR
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 ALA 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B ALA* 4.1 21.5 - - + +
111B LYS* 5.3 1.3 - - + +
112B MET* 6.3 0.9 - - + -
115B LEU* 3.9 24.1 - - + +
117B THR* 4.8 3.1 - - + -
119B ASP 5.0 5.2 - - - +
120B LEU 5.1 1.8 - - - +
121B GLU 2.8 7.7 + - - +
122B ALA* 1.3 75.8 - - - +
124B ALA* 1.3 64.8 + - - +
125B ARG* 3.1 6.5 - - - +
126B MET* 3.1 18.8 + - - +
127B ILE* 3.2 22.3 + - + +
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Residues in contact with ALA 124 (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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104B VAL* 3.8 34.9 - - + +
108B ALA* 3.9 11.1 - - + +
121B GLU 3.9 7.1 + - - +
123B ALA* 1.3 73.6 - - - +
125B ARG* 1.3 59.2 + - + +
126B MET 3.1 9.0 + - - -
127B ILE 4.1 0.4 - - - -
128B ALA* 3.6 26.5 + - - +
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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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119B ASP* 4.9 0.6 + - - -
121B GLU* 3.5 48.1 + - - +
122B ALA* 3.5 26.1 - - - +
123B ALA 3.1 2.6 - - - +
124B ALA* 1.3 81.5 - - + +
126B MET* 1.3 56.9 + - - +
128B ALA* 5.1 0.9 - - - -
129B GLY* 5.1 4.8 + - - -
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Residues in contact with MET 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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115B LEU* 3.8 35.2 - - + -
117B THR* 5.4 7.4 - - + -
123B ALA* 3.1 9.8 + - - +
124B ALA 3.1 0.4 - - - -
125B ARG* 1.3 80.9 - - + +
127B ILE* 1.3 61.1 + - + +
128B ALA 3.5 0.9 - - - -
129B GLY* 3.7 4.1 + - - +
130B SER* 3.1 27.5 + - - -
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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
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74B ALA* 4.6 16.4 - - + -
78B ILE* 4.8 8.9 - - + +
104B VAL* 3.8 26.5 - - + -
107B ILE* 3.9 21.1 - - + +
108B ALA* 3.8 11.4 - - - -
111B LYS* 3.8 30.3 - - + -
115B LEU* 4.1 13.5 - - + -
123B ALA 3.2 22.1 + - - +
124B ALA 3.8 0.4 + - - +
126B MET* 1.3 76.8 - - + +
128B ALA* 1.3 59.7 + - - +
130B SER* 3.3 7.4 + - - -
131B ALA* 2.9 27.8 + - + +
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Residues in contact with ALA 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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100B THR* 5.3 13.0 + - + +
103B GLN* 6.0 0.2 - - - -
104B VAL* 4.1 19.2 - - + +
124B ALA 3.6 16.3 + - - +
125B ARG 5.7 0.7 - - - -
126B MET 3.5 0.2 - - - -
127B ILE* 1.3 79.0 - - - +
129B GLY* 1.3 61.0 + - - +
131B ALA* 3.4 8.9 + - - +
132B ARG* 3.4 36.4 + - - +
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Residues in contact with GLY 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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125B ARG 5.1 3.4 + - - -
126B MET* 3.7 9.8 + - - +
127B ILE 3.3 0.6 - - - -
128B ALA* 1.3 77.9 - - - +
130B SER* 1.3 60.0 + - - +
132B ARG* 3.4 41.7 + - - +
133B SER* 4.1 4.9 + - - -
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Residues in contact with SER 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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15A PRO* 5.3 9.5 - - - +
74B ALA* 6.5 1.1 - - - -
78B ILE* 4.8 4.6 - - - +
126B MET* 3.1 19.3 + - - -
127B ILE* 3.3 8.0 + - - -
129B GLY* 1.3 74.5 - - - +
131B ALA* 1.3 60.5 + - - +
133B SER* 3.5 23.3 + - - +
134B MET* 3.8 10.7 - - - +
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Residues in contact with ALA 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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78B ILE* 3.8 33.2 - - + -
100B THR* 5.0 8.5 - - + +
103B GLN* 4.7 11.2 - - - +
127B ILE* 2.9 17.5 + - + +
128B ALA* 3.5 11.2 - - - +
129B GLY 3.2 0.4 - - - -
130B SER* 1.3 76.9 - - - +
132B ARG* 1.3 62.7 + - - +
133B SER 3.3 0.5 + - - -
134B MET* 3.7 9.7 - - - +
136B VAL* 3.4 23.2 + - + +
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Residues in contact with ARG 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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100B THR* 5.6 3.6 - - + +
128B ALA* 3.4 21.8 + - - +
129B GLY* 3.5 28.5 - - - +
130B SER 3.3 0.2 - - - -
131B ALA* 1.3 77.5 - - - +
133B SER* 1.3 57.1 + - - +
134B MET 3.4 0.9 + - - -
135B GLY* 3.4 4.0 - - - -
136B VAL 3.2 32.2 + - - +
137B GLU* 5.9 0.3 - - - +
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Residues in contact with SER 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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15A PRO* 5.0 6.6 - - - +
129B GLY 4.1 4.5 + - - -
130B SER* 3.5 20.1 + - - +
131B ALA 4.0 0.4 - - - -
132B ARG* 1.3 74.7 - - - +
134B MET* 1.3 68.6 + - - +
135B GLY* 4.4 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