Contacts of the helix formed by residues 134 - 145 (chain B) in PDB entry 4UN5
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 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A U 3.7 23.3 - - - +
45A U 3.7 20.2 - - - +
128B TYR* 5.0 1.7 + - - -
132B TYR* 3.8 11.0 - - - +
133B PRO* 1.3 82.7 - - - +
135B ILE* 1.3 62.9 + - - +
136B TYR* 3.3 21.8 + - - +
137B HIS* 2.6 40.9 + - + +
138B LEU 3.7 2.8 + - - -
321B MET* 5.8 0.7 - - - +
322B ILE* 4.8 1.2 + - - +
325B TYR* 3.9 19.9 - - + +
402B GLN* 4.3 6.7 - - + +
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Residues in contact with ILE 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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45A U 3.2 21.2 + - - +
46A A 3.8 19.3 - - - +
128B TYR* 4.4 9.2 - - - +
134B THR* 1.3 73.5 - - - +
136B TYR* 1.3 71.5 + - + +
138B LEU* 3.3 27.5 + - + +
139B ARG* 2.9 28.9 + - + +
156B LEU* 4.4 22.9 - - + +
157B ALA* 4.6 2.9 - - - -
160B HIS* 3.5 49.8 - - + +
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Residues in contact with TYR 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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45A U 5.0 2.2 - - - -
46A A 4.9 0.7 - - - -
134B THR* 3.1 14.3 - - - +
135B ILE* 1.3 85.9 - - + +
137B HIS* 1.3 59.8 + - - +
139B ARG* 3.5 32.3 + - - -
140B LYS* 2.9 29.8 + - - +
160B HIS* 3.9 13.0 - + - -
317B LEU* 4.7 8.1 - - + -
318B SER* 3.5 35.8 - - - +
321B MET* 3.6 33.4 - - + -
322B ILE* 3.7 5.1 - - + +
402B GLN* 3.8 28.9 + - + -
403B ARG* 3.7 24.6 + - - -
415B HIS* 5.5 1.4 - + - -
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Residues in contact with HIS 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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131B LYS 4.8 3.1 - - - +
132B TYR* 3.8 19.1 - - + -
133B PRO* 3.5 32.9 - - + +
134B THR* 2.6 37.4 + - + +
136B TYR* 1.3 76.6 - - - +
138B LEU* 1.3 56.9 + - - +
140B LYS* 3.4 2.3 + - - +
141B LYS* 2.9 29.6 + - - +
322B ILE* 3.7 36.8 - - + +
325B TYR* 3.9 26.8 - + + -
326B ASP* 4.8 2.4 + - - -
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Residues in contact with LEU 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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128B TYR* 3.8 23.1 - - + +
132B TYR* 3.6 42.7 - - + +
134B THR 3.7 1.2 + - - -
135B ILE* 3.3 22.8 + - + +
137B HIS* 1.3 75.9 - - - +
139B ARG* 1.3 62.5 + - - +
141B LYS* 3.4 1.7 + - + +
142B LEU* 2.9 51.3 + - + +
153B LEU* 3.7 43.5 - - + +
156B LEU* 4.7 3.8 - - + -
157B ALA* 4.7 2.9 - - + +
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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 ILE* 2.9 21.6 + - + +
136B TYR* 3.5 24.7 + - - +
137B HIS 3.3 0.2 - - - -
138B LEU* 1.3 77.2 - - - +
140B LYS* 1.3 56.6 + - - +
142B LEU* 3.2 3.3 + - - +
143B VAL* 2.9 35.3 + - - +
157B ALA* 4.5 15.5 + - + -
160B HIS* 3.0 43.2 + - - -
161B MET* 3.4 32.8 - - - +
164B PHE 5.3 0.2 + - - -
317B LEU* 4.2 4.0 - - - +
318B SER* 3.3 14.4 - - - +
415B HIS* 3.1 37.8 + - - -
418B GLU* 3.1 27.7 + - - +
422B ILE* 4.1 7.4 - - + +
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Residues in contact with LYS 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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136B TYR 2.9 17.6 + - - +
137B HIS 3.7 3.6 - - - +
139B ARG* 1.3 75.7 - - - +
141B LYS* 1.3 63.3 + - - +
143B VAL* 3.1 6.1 + - - +
144B ASP* 2.9 45.0 + - - +
312B ILE* 5.1 10.8 - - - +
313B THR* 4.3 14.5 - - - +
315B ALA* 4.5 8.1 - - + +
318B SER* 4.2 5.8 - - - -
319B ALA* 4.1 26.8 + - - +
322B ILE* 3.6 26.9 - - + +
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Residues in contact with LYS 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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131B LYS* 4.3 13.5 - - - +
132B TYR* 3.6 35.0 + - + +
137B HIS 2.9 17.7 + - - +
138B LEU* 3.6 6.1 - - + +
140B LYS* 1.3 76.7 - - - +
142B LEU* 1.3 74.5 + - + +
144B ASP* 5.2 1.1 - - - -
145B SER* 3.0 62.7 + - - +
147B ASP* 4.9 12.9 + - - +
148B LYS 5.6 0.6 + - - -
149B ALA* 4.8 9.1 - - - +
426B GLN* 6.0 0.2 - - - +
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Residues in contact with LEU 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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138B LEU* 2.9 31.3 + - + +
139B ARG 3.2 0.4 + - - +
141B LYS* 1.3 89.5 - - + +
143B VAL* 1.3 60.3 + - - +
145B SER* 4.5 2.0 - - - +
149B ALA* 3.6 31.0 - - + -
153B LEU* 3.7 27.6 - - + +
154B ILE* 3.9 15.5 - - + +
157B ALA* 3.7 18.4 - - + -
422B ILE* 3.7 28.2 - - + +
425B ARG* 3.9 20.3 - - - +
426B GLN* 4.8 10.1 + - + +
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Residues in contact with VAL 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 ARG 2.9 20.9 + - - +
140B LYS 3.1 4.4 + - - +
142B LEU* 1.3 80.0 - - - +
144B ASP* 1.3 62.8 - - - +
314B LYS* 3.8 41.0 - - + +
315B ALA* 3.9 15.7 - - + -
418B GLU* 3.8 20.4 - - + +
421B ALA* 3.8 15.9 - - + +
422B ILE* 3.6 21.1 - - + +
425B ARG* 3.2 23.2 + - - +
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Residues in contact with ASP 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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140B LYS* 2.9 33.3 + - + +
141B LYS* 4.5 1.6 - - - +
143B VAL* 1.3 79.8 - - - +
145B SER* 1.3 61.7 + - - +
146B THR* 3.9 1.2 + - - +
312B ILE 4.5 3.8 - - - +
313B THR* 3.0 39.6 + - - -
314B LYS* 3.4 12.5 + - - +
425B ARG* 2.6 25.5 + - - +
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Residues in contact with SER 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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141B LYS* 3.0 41.6 + - - -
142B LEU* 4.5 1.7 - - - +
143B VAL 3.8 0.2 - - - -
144B ASP* 1.3 77.8 - - - +
146B THR* 1.3 67.4 + - - +
147B ASP* 3.1 28.3 + - - +
425B ARG* 2.9 29.5 + - - +
426B GLN* 5.3 1.3 + - - -
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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