Contacts of the helix formed by residues 138 - 148 (chain B) in PDB entry 3D8U
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 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ILE* 3.0 29.4 + - - -
113B GLU* 5.8 0.2 - - - -
115B GLU* 3.7 2.6 + - - -
116B GLU* 2.9 28.9 - - - -
137B HIS* 1.3 82.4 - - - +
139B GLN* 1.3 56.1 + - - +
141B THR* 2.6 34.0 + - - +
142B HIS* 2.6 27.8 + - - -
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Residues in contact with GLN 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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116B GLU* 4.4 0.8 + - - +
138B SER* 1.3 71.2 - - - +
140B ARG* 1.3 52.8 + - - +
142B HIS* 3.2 9.6 + - - +
143B GLN* 2.7 36.8 + - - +
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Residues in contact with ARG 140 (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 GLU* 3.2 33.6 + - + +
138B SER 3.2 0.6 - - - -
139B GLN* 1.3 76.2 - - - +
141B THR* 1.3 59.2 + - - +
143B GLN* 3.5 6.4 - - - +
144B LEU* 2.8 31.7 + - - +
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Residues in contact with THR 141 (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 GLU* 3.9 19.1 - - + +
116B GLU* 3.6 25.7 - - + +
119B LEU* 4.4 12.3 - - + -
132B LEU* 5.6 6.3 - - + -
137B HIS* 3.6 8.9 - - - +
138B SER* 2.6 53.2 + - - +
140B ARG* 1.3 70.3 - - - +
142B HIS* 1.3 67.3 + - - +
143B GLN 2.9 0.5 + - - -
144B LEU* 3.2 4.5 + - - -
145B LEU* 2.8 32.7 + - - +
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Residues in contact with HIS 142 (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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135B SER 4.7 0.6 + - - -
137B HIS* 3.4 30.8 + + + +
138B SER 2.6 38.1 + - - +
139B GLN* 3.5 8.5 - - - +
141B THR* 1.3 73.2 + - - +
143B GLN* 1.3 63.7 + - - +
146B GLU* 3.4 22.2 + - - +
160B SER* 3.5 32.8 - - - -
161B LYS* 4.6 8.2 - - + +
164B TYR* 3.5 22.1 + + - -
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Residues in contact with GLN 143 (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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139B GLN 2.7 20.1 + - - +
140B ARG* 3.5 8.5 - - - +
141B THR 2.9 0.8 + - - -
142B HIS* 1.3 69.6 - - - +
144B LEU* 1.3 58.4 + - - +
146B GLU* 2.9 4.9 + - - -
147B ALA* 2.6 41.3 + - + -
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Residues in contact with LEU 144 (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 LEU* 6.3 2.9 - - + -
120B SER* 5.8 7.6 - - - -
123B LEU* 5.3 11.4 - - + -
140B ARG 2.8 20.7 + - - +
141B THR* 3.9 3.4 - - - +
143B GLN* 1.3 71.6 - - - +
145B LEU* 1.3 52.8 + - - +
147B ALA* 3.4 5.7 - - - +
148B SER* 2.6 40.3 + - - -
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Residues in contact with LEU 145 (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 VAL* 5.4 5.8 - - + -
132B LEU* 6.2 3.4 - - + -
141B THR* 2.8 23.1 + - - +
143B GLN 3.0 0.2 + - - -
144B LEU* 1.3 75.1 - - - +
146B GLU* 1.3 57.6 + - - +
148B SER* 3.1 19.5 + - - -
149B ASN 3.5 5.2 + - - -
150B THR* 3.9 15.2 + - - +
152B VAL* 4.2 22.7 - - + -
164B TYR* 4.1 14.6 - - + +
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Residues in contact with GLU 146 (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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142B HIS 3.4 17.1 + - - +
143B GLN 2.9 4.4 + - - -
145B LEU* 1.3 74.7 - - - +
147B ALA* 1.3 61.1 + - - +
148B SER 3.3 0.2 - - - -
149B ASN* 3.7 11.8 + - - +
150B THR 5.6 0.7 - - - -
161B LYS* 5.8 3.4 - - + -
164B TYR* 4.6 16.8 + - + +
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Residues in contact with ALA 147 (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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143B GLN* 2.6 30.7 + - + +
144B LEU* 3.5 6.3 - - - +
146B GLU* 1.3 72.3 - - - +
148B SER* 1.3 58.7 + - - +
149B ASN* 3.2 5.5 + - - +
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Residues in contact with SER 148 (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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123B LEU* 5.3 11.7 - - - +
144B LEU 2.6 21.9 + - - -
145B LEU* 3.1 8.0 + - - -
147B ALA* 1.3 73.1 - - - +
149B ASN* 1.3 56.2 + - - +
150B THR* 2.6 43.9 + - - +
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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