Contacts of the helix formed by residues 187 - 196 (chain C) 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 187 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ARG* 4.4 10.8 - - - +
186C ASP* 1.3 79.1 + - - +
188C LEU* 1.3 62.1 + - + +
190C GLN* 3.5 6.0 + - - +
191C ARG* 3.2 33.1 + - - +
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A MET* 4.2 10.8 - - + -
47A MET* 3.9 16.8 - - + +
51A SER* 5.1 4.9 - - - +
57A ARG* 4.1 38.4 - - + +
60A LEU* 3.9 31.4 - - + -
61A SER* 3.5 34.1 - - - +
64A MET* 4.3 1.5 - - + +
186C ASP 3.8 4.0 - - - +
187C GLU* 1.3 77.0 - - + +
189C SER* 1.3 66.0 + - - +
190C GLN 3.1 0.2 + - - -
191C ARG* 3.1 18.9 + - - +
192C LEU* 3.0 23.4 + - - +
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Residues in contact with SER 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A MET* 4.6 11.5 - - - +
186C ASP* 3.4 25.1 + - - +
188C LEU* 1.3 77.6 - - - +
190C GLN* 1.3 66.3 + - - +
192C LEU* 3.5 8.7 + - - +
193C ALA* 3.1 26.0 + - - +
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Residues in contact with GLN 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ASP* 3.1 29.1 + - - +
187C GLU* 3.9 5.8 - - - +
188C LEU 3.1 0.6 - - - -
189C SER* 1.3 83.1 - - - +
191C ARG* 1.3 60.1 + - + +
192C LEU 3.2 0.2 - - - -
193C ALA* 3.3 11.5 + - - +
194C ARG* 2.9 34.6 + - - +
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Residues in contact with ARG 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A SER* 3.7 28.7 + - - +
64A MET* 3.4 24.6 - - + +
65A ASP* 2.6 29.3 + - - +
68A GLU* 2.9 42.8 + - - +
187C GLU* 3.2 23.1 + - + +
188C LEU* 3.1 15.3 + - - +
190C GLN* 1.3 75.7 - - + +
192C LEU* 1.3 53.0 + - - +
194C ARG* 3.3 22.8 + - - +
195C LEU* 2.7 35.3 + - - +
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Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.7 30.1 - - + -
43A MET* 4.6 4.9 - - + -
44A GLN* 4.7 20.2 - - + +
47A MET* 3.6 32.3 - - + -
64A MET* 3.5 16.0 - - + +
188C LEU 3.0 12.3 + - - +
189C SER* 3.5 10.8 - - - +
190C GLN 3.2 0.2 - - - -
191C ARG* 1.3 73.9 - - - +
193C ALA* 1.3 60.6 + - - +
195C LEU* 3.0 5.8 + - + +
196C ARG* 2.8 41.2 + - + +
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Residues in contact with ALA 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C SER 3.1 14.2 + - - +
190C GLN* 3.3 15.0 + - - +
192C LEU* 1.3 80.6 - - - +
194C ARG* 1.3 61.4 + - - +
196C ARG* 5.1 0.7 - - - -
197C ASP 3.4 2.9 + - - -
198C GLN* 3.2 48.1 + - + +
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Residues in contact with ARG 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLU* 3.5 27.7 + - - -
71A LYS* 3.1 13.0 + - - -
190C GLN* 2.9 22.4 + - - +
191C ARG* 3.7 24.7 + - - +
193C ALA* 1.3 74.3 - - - +
195C LEU* 1.3 67.3 + - - +
197C ASP* 3.2 8.1 + - - -
198C GLN 5.1 2.2 - - - +
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Residues in contact with LEU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 3.3 22.4 + - - +
40A LEU* 4.0 15.5 - - + -
64A MET* 3.7 11.7 - - + -
67A LEU* 3.6 36.3 - - + -
68A GLU* 4.0 28.3 - - + +
71A LYS* 2.6 59.5 + - + +
80A ILE* 6.1 0.2 - - - +
191C ARG 2.7 22.4 + - - +
192C LEU* 3.2 6.7 - - + +
194C ARG* 1.3 73.9 - - - +
196C ARG* 1.3 58.1 + - + +
197C ASP* 3.1 0.3 + - - +
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Residues in contact with ARG 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 5.0 3.1 - - - +
37A TYR* 5.6 1.2 - - - -
40A LEU* 3.6 42.2 - - + +
44A GLN* 2.9 34.6 + - - +
83A GLU* 3.5 33.3 + - - +
130A VAL* 2.8 30.3 + - - +
131A PHE* 4.9 3.0 - - - +
192C LEU* 2.8 27.3 + - + +
193C ALA* 3.7 3.4 - - - +
194C ARG 3.3 0.4 - - - -
195C LEU* 1.3 77.2 - - + +
197C ASP* 1.3 70.2 + - - +
198C GLN* 3.3 14.0 + - + +
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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