Contacts of the helix formed by residues 165 - 177 (chain A) in PDB entry 3UNE
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 ASN 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ALA 4.9 0.2 + - - -
161A ALA* 5.6 0.2 - - - +
163A GLY 3.7 0.6 + - - -
164A LYS* 1.3 80.5 - - - +
166A TYR* 1.3 65.3 + - - +
167A VAL* 3.2 10.9 - - - +
168A ASN* 3.4 21.7 + - + +
169A GLY* 3.2 17.0 + - - -
197A SER* 3.5 30.1 + - - +
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Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 4.1 23.4 - - + +
161A ALA* 3.5 24.4 - - - +
162A MET* 4.0 10.3 - - - -
163A GLY 3.3 21.5 - - - +
164A LYS 3.4 1.0 - - - -
165A ASN* 1.3 76.3 - - - +
167A VAL* 1.3 81.4 + - + +
169A GLY* 3.7 1.7 - - - +
170A LYS* 3.2 52.5 + - - +
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ASN* 4.6 6.7 - - - +
166A TYR* 1.3 106.8 - - + +
168A ASN* 1.3 71.6 + - - +
169A GLY 3.4 0.2 - - - -
170A LYS* 4.1 6.4 + - - +
171A THR* 2.9 31.5 + - - +
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Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ASN* 3.4 27.8 + - + +
166A TYR 3.3 0.2 - - - -
167A VAL* 1.3 89.4 - - - +
169A GLY* 1.3 63.9 + - - +
171A THR* 3.0 15.6 + - - -
172A PHE* 3.3 15.2 + - - +
196A GLU* 4.6 11.5 - - + +
197A SER* 4.9 5.6 + - - +
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Residues in contact with GLY 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ALA* 4.1 13.0 - - - -
165A ASN 3.2 12.1 + - - -
166A TYR 3.4 3.7 + - - -
167A VAL 3.4 0.2 - - - -
168A ASN* 1.3 76.2 - - - +
170A LYS* 1.3 58.5 + - - +
172A PHE* 3.2 8.3 + - - +
173A LEU* 2.8 37.3 + - - +
193A THR* 5.0 9.5 - - - +
196A GLU* 5.6 4.3 - - - -
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLN* 5.8 1.2 - - - +
157A TRP* 4.1 18.1 - - + -
159A ALA 5.2 1.6 - - - +
160A THR* 3.7 18.1 + - - +
161A ALA 3.9 26.2 + - - +
166A TYR* 3.2 41.2 + - - +
167A VAL* 4.7 5.8 - - - +
168A ASN 3.6 0.2 - - - -
169A GLY* 1.3 75.9 - - - +
171A THR* 1.3 58.5 + - + +
173A LEU* 3.5 7.9 - - + +
174A GLU* 2.9 33.1 + - - +
53B HIS* 4.1 32.8 - - + +
55B LEU* 4.2 3.9 - - + +
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Residues in contact with THR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A VAL 2.9 22.2 + - - +
168A ASN* 3.0 17.0 + - - -
170A LYS* 1.3 76.5 - - + +
172A PHE* 1.3 58.9 + - - +
174A GLU* 3.4 32.2 - - - +
175A LYS* 3.5 20.9 - - - +
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Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ASN 3.3 15.0 + - - +
169A GLY* 3.2 5.3 + - - +
171A THR* 1.3 79.0 + - - +
173A LEU* 1.3 59.3 + - - +
174A GLU 3.5 0.2 - - - -
175A LYS* 3.5 16.9 + - + +
176A ARG* 3.2 66.8 + - + +
189A THR 5.3 0.4 - - - -
192A LEU* 4.2 12.6 - - + -
193A THR* 3.6 36.6 - - + -
196A GLU* 3.3 37.7 - - + +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 4.2 4.9 - - + -
37A ILE* 3.8 26.0 - - + -
159A ALA* 3.8 14.8 - - + +
160A THR* 3.6 36.3 - - - +
161A ALA* 3.8 8.5 - - + +
169A GLY* 2.8 25.6 + - - +
170A LYS* 3.5 8.3 - - - +
172A PHE* 1.3 75.0 - - - +
174A GLU* 1.3 56.2 + - - +
175A LYS 3.0 4.7 - - - -
176A ARG* 4.9 1.3 - - + -
177A TYR* 2.6 42.6 + - + +
189A THR* 5.5 1.6 - - - +
193A THR* 3.8 22.9 - - + -
55B LEU* 4.2 11.2 - - + -
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Residues in contact with GLU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LYS 2.9 17.1 + - - +
171A THR* 3.4 35.8 - - - +
173A LEU* 1.3 74.6 - - - +
175A LYS* 1.3 59.7 + - + +
177A TYR* 4.6 7.0 - - - +
53B HIS* 5.1 7.0 + - - -
54B LYS* 3.7 46.9 + - + +
55B LEU* 3.6 23.0 - - + +
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Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A THR* 3.5 19.7 - - - +
172A PHE* 3.5 17.7 + - + +
173A LEU 3.0 0.6 - - - -
174A GLU* 1.3 82.8 - - + +
176A ARG* 1.3 60.1 + - + +
177A TYR 5.1 0.4 - - - -
178A ASN* 5.4 0.9 - - - +
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Residues in contact with ARG 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PHE* 3.2 52.7 + - + +
173A LEU* 3.1 4.1 + - + +
175A LYS* 1.3 81.7 + - - +
177A TYR* 1.3 64.7 + - - +
178A ASN* 3.1 15.8 + - - +
181A LEU* 5.1 3.5 - - - +
189A THR* 3.5 25.7 + - - +
192A LEU* 3.9 27.4 - - + +
193A THR* 5.9 0.4 - - + -
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.7 22.4 - - + -
38A LYS* 3.2 32.1 + - - +
39A ALA* 5.4 1.2 - - - -
158A LYS* 3.4 43.8 + - + +
159A ALA* 4.0 10.8 - - + -
173A LEU* 2.6 30.5 + - + +
174A GLU* 4.6 7.7 - - - +
175A LYS 5.1 0.3 - - - -
176A ARG* 1.3 74.1 - - - +
178A ASN* 1.3 91.1 + - - +
179A GLU* 4.6 12.8 - - + +
181A LEU* 4.3 11.2 - - + -
189A THR* 5.1 5.3 + - + +
55B LEU* 3.8 19.5 - - + -
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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