Contacts of the helix formed by residues 129 - 139 (chain B) in PDB entry 3JCA
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 SER 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B THR* 3.8 26.7 + - - +
125B PRO 3.2 5.8 + - - -
127B TYR 3.4 0.8 - - - -
128B VAL* 1.3 83.7 - - - +
130B ARG* 1.3 60.8 + - - +
131B SER* 2.8 27.0 + - - -
132B ILE* 2.9 26.4 + - - +
133B GLN 3.1 7.3 + - - -
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Residues in contact with ARG 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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128B VAL* 3.3 0.8 + - - +
129B SER* 1.3 74.1 + - - +
131B SER* 1.3 58.3 + - - +
132B ILE 3.1 0.2 - - - -
133B GLN* 3.2 28.2 + - + +
134B GLU* 2.8 27.7 + - - +
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Residues in contact with SER 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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99B THR* 4.8 4.9 + - - -
100B LYS* 5.4 7.9 + - - -
103B LEU* 4.5 6.4 - - - +
129B SER* 2.8 22.4 + - - -
130B ARG* 1.3 77.9 - - - +
132B ILE* 1.3 66.1 + - - +
134B GLU* 3.3 14.1 - - - +
135B PHE* 3.0 37.4 + - - -
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Residues in contact with ILE 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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99B THR* 3.8 20.0 - - - +
102B VAL* 4.7 7.9 - - + -
103B LEU* 3.9 29.6 - - + -
106B LEU* 5.8 3.4 - - + -
126B ALA 3.0 30.3 - - - +
127B TYR* 3.7 25.4 - - + +
129B SER* 2.9 12.8 + - - +
131B SER* 1.3 78.5 - - - +
133B GLN* 1.3 61.9 + - - +
135B PHE* 3.0 8.8 + - + +
136B LEU* 2.8 43.7 + - + +
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Residues in contact with GLN 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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127B TYR 5.0 2.7 - - - +
128B VAL* 2.8 29.0 + - - +
129B SER 3.1 7.2 + - - +
130B ARG* 3.4 29.9 - - + +
132B ILE* 1.3 76.5 - - - +
134B GLU* 1.3 56.2 + - - +
136B LEU* 3.2 17.1 + - + +
137B ALA* 2.9 28.5 + - - +
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Residues in contact with GLU 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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130B ARG 2.8 13.1 + - - +
131B SER* 3.3 18.2 - - - +
133B GLN* 1.3 75.1 - - - +
135B PHE* 1.3 62.6 - - - +
137B ALA* 3.0 9.5 + - + +
138B ARG* 2.8 67.4 + - + +
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Residues in contact with PHE 135 (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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182A HIS* 5.1 16.4 - + - -
100B LYS* 5.0 9.6 - - - -
103B LEU* 3.6 37.2 - - + -
106B LEU* 5.5 0.9 - - + -
131B SER* 3.0 23.5 + - - -
132B ILE* 3.0 9.1 + - + +
134B GLU* 1.3 80.7 - - + +
136B LEU* 1.3 60.8 + - - +
138B ARG* 3.2 26.7 + - - +
139B TRP* 2.9 74.3 + + + -
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Residues in contact with LEU 136 (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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106B LEU* 5.4 8.5 - - + -
119B ILE* 5.0 8.1 - - + -
127B TYR 5.7 1.3 - - - +
132B ILE* 2.8 33.6 + - + +
133B GLN* 3.4 19.1 - - + +
135B PHE* 1.3 75.4 - - + +
137B ALA* 1.3 58.8 + - - +
139B TRP* 3.3 1.9 + - - +
140B LYS* 2.8 24.6 + - - -
141B ILE* 2.8 55.7 + - + +
142B SER 5.4 0.2 - - - +
143B HIS* 3.9 36.6 - - + -
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Residues in contact with ALA 137 (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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133B GLN 2.9 12.9 + - - +
134B GLU* 3.3 12.3 - - + +
136B LEU* 1.3 77.0 - - - +
138B ARG* 1.3 62.3 + - + +
140B LYS* 3.1 32.5 + - - +
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Residues in contact with ARG 138 (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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134B GLU* 2.8 48.6 + - + +
135B PHE* 3.2 35.1 + - - +
137B ALA* 1.3 77.3 - - - +
139B TRP* 1.3 63.7 + - + +
140B LYS* 3.6 9.9 + - - +
7E GLU* 5.4 3.6 - - - +
11E LEU* 3.1 51.6 - - + +
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Residues in contact with TRP 139 (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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182A HIS* 5.6 7.9 - - - -
186A HIS* 5.9 6.7 - + - -
103B LEU* 4.9 3.8 - - + -
106B LEU* 3.8 17.9 - - + -
107B ALA* 5.9 5.6 - - + -
110B PHE* 3.5 34.3 - + - -
115B ILE* 3.8 23.5 - - + +
116B PRO 4.6 1.0 - - - +
135B PHE* 2.9 65.5 + + + +
136B LEU* 4.9 0.9 - - + -
138B ARG* 1.3 81.5 - - + +
140B LYS* 1.3 71.7 + - - +
141B ILE* 3.1 25.8 + - + +
11E LEU* 3.7 14.6 - - + +
12E HIS* 3.3 38.9 + + - -
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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