Contacts of the helix formed by residues 133 - 142 (chain B) in PDB entry 1UKW
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 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ALA 4.9 2.9 - - - +
132B GLY* 1.3 75.0 - - - -
134B GLU* 1.3 60.3 + - - +
135B GLU* 3.5 10.1 + - - +
136B GLN* 2.9 39.4 + - - +
137B LYS* 2.8 32.3 + - - +
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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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90B TYR* 4.2 12.8 - - + +
133B THR* 1.3 74.2 - - - +
135B GLU* 1.3 62.6 + - - +
137B LYS* 3.3 12.5 + - + +
138B GLU* 3.0 27.3 + - - +
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Residues in contact with GLU 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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133B THR* 3.5 9.0 + - - +
134B GLU* 1.3 79.1 - - - +
136B GLN* 1.3 68.5 + - - +
138B GLU* 3.5 5.6 + - - +
139B ARG* 2.6 81.7 + - - +
252B GLU* 4.6 3.5 - - - +
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Residues in contact with GLN 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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128B VAL* 4.4 1.3 - - + -
131B ALA 4.4 0.9 - - - +
132B GLY* 3.1 14.1 - - - -
133B THR* 2.9 43.0 + - - +
135B GLU* 1.3 86.1 - - - +
137B LYS* 1.3 59.4 + - - +
139B ARG* 4.0 8.1 - - - +
140B PHE* 2.7 52.0 + - + +
251B VAL 5.0 0.2 + - - -
252B GLU* 3.1 24.8 + - - +
253B ASN* 4.2 1.2 - - - +
254B ARG 3.0 31.5 + - - +
255B LEU* 4.1 8.6 - - + +
256B GLY 5.2 0.5 + - - -
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Residues in contact with LYS 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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90B TYR* 3.3 39.2 + - + +
128B VAL* 3.8 18.8 - - - +
129B LEU* 3.6 30.0 + - + +
132B GLY 3.4 19.8 + - - +
133B THR 2.8 28.1 + - - +
134B GLU* 3.6 4.6 - - + +
136B GLN* 1.3 70.3 - - - +
138B GLU* 1.3 55.5 + - - +
141B LEU* 2.7 54.8 + - + +
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Residues in contact with GLU 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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89B GLU 4.3 0.2 - - - +
90B TYR* 3.5 18.0 - - + -
134B GLU 3.0 17.5 + - - +
135B GLU* 3.7 6.1 - - - +
137B LYS* 1.3 75.5 - - - +
139B ARG* 1.3 61.0 + - - +
142B ARG* 2.7 82.8 + - - +
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Residues in contact with ARG 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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135B GLU* 2.6 66.9 + - - +
136B GLN* 3.7 9.0 - - - +
138B GLU* 1.3 80.0 - - - +
140B PHE* 1.3 77.4 + - + +
143B PRO* 3.2 24.4 - - - +
217B GLU* 4.6 4.2 + - - -
250B PRO* 5.5 0.4 - - - +
252B GLU* 3.2 29.2 + - - +
253B ASN* 2.4 32.3 + - - -
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Residues in contact with PHE 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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128B VAL* 4.3 9.6 - - + -
136B GLN* 2.7 47.6 + - + +
139B ARG* 1.3 98.4 - - + +
141B LEU* 1.3 66.2 + - + +
143B PRO* 3.9 2.8 - - - +
144B LEU* 3.7 12.5 - - - +
195B TRP* 3.1 45.3 + + + +
215B VAL* 3.5 42.8 - - + -
217B GLU* 3.9 15.0 - - - -
253B ASN* 3.2 31.2 - - - -
255B LEU* 4.5 4.3 - - + -
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Residues in contact with LEU 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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86B ILE* 3.5 42.3 - - + +
90B TYR* 4.2 9.4 - - + -
125B ILE* 4.7 11.0 - - + -
128B VAL* 3.8 26.2 - - + -
129B LEU* 3.8 29.8 - - + -
137B LYS* 2.7 41.5 + - + +
140B PHE* 1.3 82.2 - - + +
142B ARG* 1.3 64.4 + - - +
143B PRO 3.4 0.9 - - - -
144B LEU* 3.0 17.6 + - + +
145B THR* 3.5 4.5 + - - +
195B TRP* 4.3 9.2 - - + -
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Residues in contact with ARG 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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89B GLU 3.1 19.0 + - - -
90B TYR* 3.4 29.3 + - - +
91B GLY* 3.7 6.1 - - - +
137B LYS 3.9 0.2 + - - -
138B GLU* 2.7 61.1 + - - +
141B LEU* 1.3 77.2 - - - +
143B PRO* 1.3 64.9 - - + +
144B LEU 3.0 4.0 + - - -
145B THR* 2.7 24.2 + - - -
146B GLU* 3.2 38.8 - - - +
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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