Contacts of the helix formed by residues 186 - 195 (chain D) in PDB entry 4UN7
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 PRO 186 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D TYR* 3.9 8.0 - - + +
111D LYS* 3.4 32.8 - - + -
115D VAL* 3.6 20.4 - - + -
178D LEU* 3.3 25.6 - - + +
184D PRO 3.5 3.1 - - - +
185D LEU* 1.3 91.1 - - + +
187D PRO* 1.3 71.5 - - + +
188D GLU* 3.4 3.4 - - + +
189D ALA* 3.3 12.5 + - + +
190D ALA* 3.0 24.9 + - - +
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Residues in contact with PRO 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D TYR* 4.5 1.8 - - - +
47D LEU* 3.4 31.6 - - + -
51D HIS* 4.0 21.1 - - + +
115D VAL* 4.6 11.0 - - + -
186D PRO* 1.3 88.4 - - + +
188D GLU* 1.3 62.3 + - + +
190D ALA* 4.0 5.3 - - + +
191D ALA* 3.1 28.6 + - - +
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Residues in contact with GLU 188 (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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120D LYS* 2.8 52.7 - - - +
122D LEU* 4.7 15.0 - - + +
186D PRO* 3.4 2.5 - - + +
187D PRO* 1.3 81.7 - - + +
189D ALA* 1.3 59.2 + - - +
191D ALA* 4.1 7.7 - - - +
192D LEU* 3.2 31.0 + - - +
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Residues in contact with ALA 189 (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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174D VAL* 6.5 0.2 - - + -
178D LEU* 3.4 31.6 - - + +
179D SER* 4.0 16.1 + - - +
185D LEU* 4.1 9.0 - - + -
186D PRO* 3.3 18.6 + - + +
187D PRO 3.2 0.2 - - - -
188D GLU* 1.3 77.0 - - - +
190D ALA* 1.3 57.8 + - - +
191D ALA 3.1 1.3 - - - -
192D LEU* 2.8 33.3 + - - +
193D GLU* 3.5 8.7 + - - +
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Residues in contact with ALA 190 (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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185D LEU* 4.5 13.1 - - + +
186D PRO 3.0 14.7 + - - +
187D PRO* 4.1 5.8 - - + +
189D ALA* 1.3 77.9 - - - +
191D ALA* 1.3 61.4 + - - +
193D GLU* 3.5 15.5 - - - +
194D HIS* 3.1 36.7 + - + +
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Residues in contact with ALA 191 (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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187D PRO 3.1 19.4 + - - +
188D GLU* 4.1 8.3 - - - +
189D ALA 3.1 0.2 - - - -
190D ALA* 1.3 78.6 - - - +
192D LEU* 1.3 57.9 + - + +
193D GLU 3.2 0.7 - - - -
194D HIS* 4.1 1.7 - - - -
195D HIS* 3.1 34.9 + - - +
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Residues in contact with LEU 192 (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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122D LEU* 4.2 24.0 - - + -
174D VAL* 4.8 12.6 - - + -
179D SER* 5.8 3.1 - - - +
188D GLU 3.2 20.9 - - - +
189D ALA* 2.8 19.2 + - - +
191D ALA* 1.3 73.9 - - + +
193D GLU* 1.3 58.4 + - - +
195D HIS* 4.2 16.8 + - - +
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Residues in contact with GLU 193 (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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179D SER* 6.3 0.9 - - - -
181D HIS* 3.0 39.7 + - - -
185D LEU* 3.8 15.3 - - - +
189D ALA 4.0 6.5 - - - +
190D ALA* 3.5 18.7 - - - +
192D LEU* 1.3 79.8 - - - +
194D HIS* 1.3 74.7 + - + +
195D HIS* 3.0 25.3 - - - -
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Residues in contact with HIS 194 (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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190D ALA* 3.1 29.7 + - + +
191D ALA* 4.7 2.0 - - - +
193D GLU* 1.3 90.4 - - + +
195D HIS* 1.3 76.2 + - - +
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Residues in contact with HIS 195 (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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191D ALA* 3.1 22.5 + - - +
192D LEU* 4.2 15.3 + - - +
193D GLU* 3.0 22.5 + - - -
194D HIS* 1.3 89.4 + - - +
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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