Contacts of the helix formed by residues 165 - 175 (chain D) in PDB entry 3UNF
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 ALA 165 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D THR* 3.4 20.1 - - + +
161D ALA* 5.2 0.7 - - - +
162D ILE 5.6 0.2 - - - -
163D GLY 4.3 1.1 - - - -
164D SER* 1.3 76.9 + - - +
166D SER* 1.3 61.8 + - - +
167D GLU 3.8 0.9 - - - +
168D GLY* 4.4 5.4 - - - +
169D ALA* 3.6 19.5 + - - +
197D VAL* 3.7 37.0 - - + +
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Residues in contact with SER 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LYS* 5.8 5.7 - - - +
161D ALA* 4.4 9.6 - - - +
162D ILE* 4.4 9.4 - - - +
163D GLY 3.5 27.6 + - - +
164D SER 3.4 5.0 + - - -
165D ALA* 1.3 74.9 - - - +
167D GLU* 1.3 73.6 + - - +
168D GLY 3.3 0.4 - - - -
169D ALA* 3.5 3.1 + - - +
170D GLN* 2.9 33.4 + - - +
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Residues in contact with GLU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D SER* 1.3 84.0 + - - +
168D GLY* 1.3 65.1 + - - +
170D GLN* 3.6 7.3 - - + +
171D SER* 3.1 24.9 + - - -
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Residues in contact with GLY 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D ALA* 4.4 4.2 - - - +
166D SER 3.3 2.4 - - - +
167D GLU* 1.3 79.9 - - - +
169D ALA* 1.3 57.3 + - - +
171D SER* 2.9 20.6 + - - -
172D SER* 3.2 14.0 + - - -
197D VAL* 4.2 14.3 - - - +
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Residues in contact with ALA 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D THR* 5.7 1.3 - - - +
30D ILE* 4.3 7.4 - - + -
161D ALA* 3.7 20.4 - - + -
165D ALA 3.6 20.2 + - - +
166D SER 3.5 1.4 + - - -
167D GLU 3.4 0.2 - - - -
168D GLY* 1.3 73.5 - - - +
170D GLN* 1.3 60.0 + - - +
172D SER* 3.4 1.4 + - - -
173D LEU* 3.0 35.4 + - - +
193D ILE* 3.8 25.2 - - + +
197D VAL* 4.0 10.7 - - + +
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Residues in contact with GLN 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ALA 4.0 12.7 + - - -
160D ARG* 3.0 38.1 + - - +
161D ALA* 3.6 17.5 + - - +
166D SER* 2.9 17.3 + - - +
167D GLU* 3.6 10.1 - - - +
169D ALA* 1.3 77.7 - - - +
171D SER* 1.3 56.6 + - - +
173D LEU* 3.6 8.6 + - - +
174D GLN* 3.1 31.4 + - - +
51E SER* 3.8 26.8 + - - -
53E LEU* 4.2 10.4 - - - +
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Residues in contact with SER 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D GLU 3.1 13.1 + - - -
168D GLY* 2.9 18.4 + - - -
170D GLN* 1.3 73.8 - - - +
172D SER* 1.3 64.5 + - - +
174D GLN* 3.2 26.5 + - - +
175D GLU* 3.2 26.1 + - - +
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Residues in contact with SER 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D GLY 3.2 15.7 + - - -
169D ALA 3.7 5.4 - - - -
171D SER* 1.3 84.2 + - - +
173D LEU* 1.3 57.5 + - - +
175D GLU* 4.1 1.8 + - - +
176D VAL* 3.2 30.9 + - - +
193D ILE* 3.8 29.4 - - - +
196D GLN* 3.6 17.9 + - - -
197D VAL* 5.5 1.4 - - - +
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Residues in contact with LEU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 3.9 22.2 - - + -
32D ILE* 3.9 32.8 - - + -
159D ALA* 4.1 13.9 - - + -
160D ARG* 4.1 24.9 - - - +
161D ALA* 4.1 7.4 - - + +
169D ALA 3.0 21.5 + - - +
170D GLN* 3.8 9.2 - - - +
172D SER* 1.3 75.0 - - - +
174D GLN* 1.3 64.9 + - - +
176D VAL* 3.5 3.2 - - - +
177D TYR* 3.2 32.6 + - + +
189D SER* 5.6 1.8 - - - -
193D ILE* 3.8 20.0 - - + -
53E LEU* 4.5 6.3 - - + -
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Residues in contact with GLN 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D GLN* 3.1 17.0 + - - +
171D SER* 3.2 24.7 + - - +
173D LEU* 1.3 78.4 - - - +
175D GLU* 1.3 63.6 + - + +
177D TYR* 4.3 7.1 + - - +
51E SER* 5.4 4.4 - - - +
52E GLU* 3.3 55.6 + - + +
53E LEU* 3.7 15.4 - - + +
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Residues in contact with GLU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D SER* 3.2 26.7 + - - +
172D SER* 4.9 1.6 - - - +
173D LEU 3.3 0.2 - - - -
174D GLN* 1.3 81.4 - - + +
176D VAL* 1.3 66.3 + - + +
177D TYR 3.6 1.5 + - - -
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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