Contacts of the helix formed by residues 137 - 148 (chain L) in PDB entry 3Q2K
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 THR 137 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135L ASN* 2.9 31.9 + - + +
138L LEU* 1.3 69.4 + - - +
139L GLN* 3.2 2.5 - - - +
140L LEU* 3.3 18.6 + - + +
141L VAL* 3.0 28.3 + - - +
263L VAL* 3.5 9.6 - - - +
268L VAL 2.8 24.8 + - - +
269L ASN* 4.2 20.9 - - - +
271L ILE* 3.7 29.6 - - + +
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Residues in contact with LEU 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132L ASN* 3.3 35.7 - - + +
133L ARG* 4.5 2.0 - - - +
135L ASN* 3.5 13.7 + - + +
137L THR* 1.3 83.9 + - - +
139L GLN* 1.3 55.9 + - - +
141L VAL* 2.9 11.7 + - + +
142L LYS* 2.8 36.1 + - - +
195L LEU* 4.1 30.3 - - + -
198L TRP* 4.3 15.3 - - + -
199L LEU* 4.0 7.5 - - + +
252L ILE* 4.8 5.8 - - + -
263L VAL* 4.8 3.8 - - + -
268L VAL* 3.8 40.8 - - + +
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Residues in contact with GLN 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133L ARG* 2.4 30.9 + - - +
134L ARG* 2.8 48.2 + - - +
135L ASN 3.1 10.2 + - - +
137L THR 4.7 1.3 - - - +
138L LEU* 1.3 77.4 - - - +
140L LEU* 1.3 64.4 + - + +
142L LYS* 3.2 8.0 + - - +
143L LYS* 2.9 54.7 + - - +
198L TRP* 3.7 16.9 - - - -
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Residues in contact with LEU 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L THR* 3.3 19.4 + - + +
138L LEU 3.2 0.4 - - - -
139L GLN* 1.3 79.0 - - + +
141L VAL* 1.3 63.7 + - - +
143L LYS* 3.1 14.9 + - + +
144L ALA* 2.9 22.3 + - - +
271L ILE* 3.9 24.2 - - + -
274L TRP* 3.9 23.3 - - + -
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Residues in contact with VAL 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L THR 3.0 17.9 - - - +
138L LEU* 2.9 11.4 + - + +
140L LEU* 1.3 74.1 - - - +
142L LYS* 1.3 64.5 + - - +
144L ALA* 2.9 6.2 + - - +
145L ILE* 2.9 42.2 + - + +
150L PHE* 4.8 9.0 - - + -
199L LEU* 4.1 12.3 - - + -
252L ILE* 5.9 1.1 - - + -
254L ILE* 3.9 19.1 - - + -
261L VAL* 4.6 10.8 - - + -
263L VAL* 3.8 25.8 - - + -
271L ILE* 5.9 0.4 - - + -
274L TRP* 4.5 9.4 - - + -
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Residues in contact with LYS 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138L LEU 2.8 11.7 + - - +
139L GLN* 3.6 9.2 - - - +
141L VAL* 1.3 78.5 - - - +
143L LYS* 1.3 61.4 + - + +
145L ILE* 3.5 4.7 + - + +
146L GLU* 3.1 64.9 + - - +
198L TRP* 3.1 56.6 + - + +
199L LEU* 3.3 35.2 + - + +
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Residues in contact with LYS 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L GLN* 2.9 43.6 + - - +
140L LEU* 3.8 14.4 - - + +
142L LYS* 1.3 76.7 - - + +
144L ALA* 1.3 63.8 + - - +
146L GLU* 3.8 11.6 - - - +
147L GLN* 3.0 47.0 + - - +
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Residues in contact with ALA 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140L LEU 2.9 14.1 + - - +
141L VAL* 2.9 8.2 + - - +
143L LYS* 1.3 77.7 - - - +
145L ILE* 1.3 59.8 + - - +
147L GLN* 3.6 9.2 + - - +
148L GLY 3.6 2.1 + - - -
149L ARG* 3.2 34.7 + - - +
150L PHE* 4.1 8.1 - - + -
274L TRP* 4.0 21.1 - - + -
276L PHE* 4.1 20.4 - - + -
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Residues in contact with ILE 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L VAL* 2.9 39.0 + - + +
142L LYS* 3.9 7.2 - - + +
144L ALA* 1.3 72.5 - - - +
146L GLU* 1.3 66.2 - - + +
148L GLY* 2.9 23.0 + - - -
149L ARG 4.2 0.5 + - - -
150L PHE* 3.4 27.9 + - + +
153L ILE* 4.5 19.3 - - + -
199L LEU* 3.6 35.0 - - + +
200L VAL* 5.3 1.6 - - + +
254L ILE* 4.1 16.2 - - + -
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Residues in contact with GLU 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142L LYS* 3.1 51.5 + - - +
143L LYS* 3.8 12.1 - - - +
145L ILE* 1.3 82.4 - - + +
147L GLN* 1.3 60.5 + - + +
148L GLY* 3.3 0.7 + - - -
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Residues in contact with GLN 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143L LYS* 3.0 44.4 + - - +
144L ALA* 3.9 6.3 - - - +
145L ILE 3.0 0.6 + - - -
146L GLU* 1.3 78.0 - - + +
148L GLY* 1.3 57.6 + - - +
149L ARG* 3.5 26.2 + - + +
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Residues in contact with GLY 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L ILE 2.9 13.2 + - - -
146L GLU 3.2 1.7 - - - -
147L GLN* 1.3 78.4 - - - +
149L ARG* 1.3 65.4 + - - +
150L PHE 3.1 4.6 + - - -
151L GLY* 3.1 14.1 + - - -
258L LYS* 5.0 2.9 - - - +
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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