Contacts of the helix formed by residues 184 - 198 (chain D) in PDB entry 4TXQ
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 GLU 184 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ARG* 5.6 10.3 - - + -
183D ALA* 1.3 71.1 - - - +
185D GLN* 1.3 63.2 + - - +
186D ASP 3.3 0.9 - - - -
187D GLU* 3.4 16.0 + - + +
188D LEU* 3.2 26.9 + - + +
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Residues in contact with GLN 185 (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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47B MET* 4.1 6.1 + - + +
51B SER* 2.9 47.5 + - - +
52B LYS* 5.1 6.6 - - - +
57B ARG* 5.3 1.8 - - - +
183D ALA* 4.5 10.7 - - + +
184D GLU* 1.3 76.7 - - - +
186D ASP* 1.3 66.1 + - - +
188D LEU* 3.0 12.8 + - - +
189D SER* 2.8 32.1 + - - +
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Residues in contact with ASP 186 (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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183D ALA* 3.6 26.9 + - - +
184D GLU 3.3 0.6 - - - -
185D GLN* 1.3 79.1 - - - +
187D GLU* 1.3 60.5 + - - +
189D SER* 3.2 9.9 + - - -
190D GLN* 2.8 47.5 + - + +
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Residues in contact with GLU 187 (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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61B SER* 5.5 0.5 + - - -
183D ALA 4.2 1.9 + - - +
184D GLU* 3.4 22.4 + - + +
185D GLN 3.3 0.2 - - - -
186D ASP* 1.3 77.5 - - - +
188D LEU* 1.3 62.6 + - - +
190D GLN* 3.8 12.7 - - - +
191D ARG* 3.1 64.9 + - + +
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Residues in contact with LEU 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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43B MET* 4.3 7.7 - - + +
47B MET* 4.0 19.9 - - + +
51B SER* 5.1 2.0 - - - -
57B ARG* 3.9 25.6 - - + +
60B LEU* 3.9 26.5 - - + +
61B SER* 3.6 33.0 - - - +
64B MET* 4.1 7.0 - - + +
184D GLU* 3.2 17.3 + - + +
185D GLN* 3.0 12.0 + - - +
187D GLU* 1.3 79.9 - - - +
189D SER* 1.3 64.8 + - - +
191D ARG* 3.4 17.4 + - - +
192D LEU* 3.1 23.9 + - - +
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Residues in contact with SER 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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47B MET* 3.6 17.2 - - - +
185D GLN* 2.8 25.1 + - - +
186D ASP* 3.2 13.3 + - - -
188D LEU* 1.3 72.2 - - - +
190D GLN* 1.3 60.8 + - - +
192D LEU* 3.3 7.5 + - - +
193D ALA* 3.0 29.7 + - - +
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Residues in contact with GLN 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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186D ASP* 2.8 34.3 + - + +
187D GLU* 3.8 13.1 - - - +
189D SER* 1.3 79.0 - - - +
191D ARG* 1.3 57.9 + - + +
193D ALA* 3.5 5.5 + - - +
194D ARG* 3.1 28.2 + - - +
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Residues in contact with ARG 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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61B SER* 3.8 23.2 + - - -
64B MET* 3.5 26.1 - - + +
65B ASP* 2.7 29.7 + - - +
68B GLU* 2.9 45.5 + - - +
187D GLU* 3.1 49.1 + - + +
188D LEU* 3.9 9.6 - - - +
190D GLN* 1.3 74.6 - - + +
192D LEU* 1.3 59.9 + - - +
194D ARG* 3.6 5.9 - - - +
195D LEU* 2.9 28.1 + - - +
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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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40B LEU* 3.8 28.5 - - + -
43B MET* 4.0 10.1 - - + -
44B GLN* 4.4 29.4 - - + +
47B MET* 4.4 15.7 - - + -
64B MET* 3.5 20.8 - - + +
188D LEU 3.1 17.3 + - - +
189D SER* 3.6 7.2 - - - +
190D GLN 3.3 0.2 - - - -
191D ARG* 1.3 75.3 - - - +
193D ALA* 1.3 59.9 + - - +
195D LEU* 3.0 7.9 + - + +
196D ARG* 2.9 40.1 + - + +
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Residues in contact with ALA 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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189D SER 3.0 17.1 + - - +
190D GLN* 3.8 7.0 - - - +
191D ARG 3.4 0.2 - - - -
192D LEU* 1.3 74.9 - - - +
194D ARG* 1.3 54.0 + - - +
196D ARG* 3.1 7.0 + - - -
197D ASP* 2.7 52.1 + - - +
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Residues in contact with ARG 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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71B LYS* 4.3 0.2 + - - -
190D GLN 3.1 18.6 + - - +
191D ARG* 3.6 7.4 - - - +
193D ALA* 1.3 76.2 - - - +
195D LEU* 1.3 63.4 + - - +
197D ASP* 4.5 3.8 - - - +
198D GLN* 3.0 32.3 + - + +
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Residues in contact with LEU 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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36B TYR* 3.5 22.7 + - - +
40B LEU* 3.8 21.3 - - + -
64B MET* 4.1 7.9 - - - -
67B LEU* 3.6 53.6 - - + +
68B GLU* 4.1 15.5 - - + +
71B LYS* 2.8 41.3 + - + +
191D ARG 2.9 15.6 + - - +
192D LEU* 3.2 11.4 - - + +
194D ARG* 1.3 77.8 - - - +
196D ARG* 1.3 58.6 + - - +
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Residues in contact with ARG 196 (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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37B TYR* 5.6 0.6 - - - -
40B LEU* 3.2 44.2 - - - +
44B GLN* 3.2 24.7 + - - +
83B GLU* 3.9 39.5 + - - +
130B VAL* 2.8 36.1 + - - +
131B PHE* 4.6 4.2 - - - +
192D LEU* 2.9 26.6 + - + +
193D ALA* 3.6 7.0 - - - +
195D LEU* 1.3 80.3 - - - +
197D ASP* 1.3 69.2 + - - +
198D GLN 3.6 3.5 - - - +
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Residues in contact with ASP 197 (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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193D ALA* 2.7 36.1 + - - +
194D ARG* 4.4 2.7 - - - +
196D ARG* 1.3 79.5 - - - +
198D GLN* 1.3 66.3 + - - +
199D VAL* 3.5 7.1 + - - +
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Residues in contact with GLN 198 (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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71B LYS* 2.7 30.7 + - - +
83B GLU* 5.6 1.0 - - - +
194D ARG* 3.0 20.0 + - + +
195D LEU 4.0 1.4 - - - +
196D ARG 4.0 2.8 - - - +
197D ASP* 1.3 79.2 - - - +
199D VAL* 1.3 61.9 + - - +
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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