Contacts of the helix formed by residues 194 - 204 (chain A) in PDB entry 1EQR
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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A THR* 3.3 34.1 - - + +
163A PRO 6.0 0.4 - - - +
191A PRO* 5.5 4.3 - - + -
193A SER* 1.3 85.1 - - - +
195A GLN* 1.3 54.9 + - - +
196A LEU 3.4 1.6 - - - -
197A PHE* 3.1 13.2 + - + -
198A LYS* 2.8 34.3 + - - +
209A TYR* 3.5 7.0 - - + +
211A GLN* 3.9 2.0 - - - +
213A VAL* 3.5 32.1 - - + -
214A LYS 5.4 0.4 - - - +
215A CYS* 4.5 2.0 - - - -
233A ASP* 3.2 29.8 - - - +
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Residues in contact with GLN 195 (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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169A THR* 4.3 16.8 + - - +
192A GLN* 5.4 9.3 - - - +
193A SER* 2.9 34.6 + - - +
194A PRO* 1.3 77.3 - - - +
196A LEU* 1.3 76.5 + - + +
198A LYS* 3.6 24.4 - - - +
199A GLN* 3.6 18.0 + - - +
233A ASP* 5.5 0.2 + - - -
449A HIS* 5.2 15.3 + - + +
450A PRO* 6.0 0.2 - - - +
451A PHE* 4.9 18.9 - - + -
514A PHE* 6.3 0.4 - - - -
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Residues in contact with LEU 196 (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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169A THR* 5.7 3.4 - - + -
194A PRO 3.4 0.2 - - - -
195A GLN* 1.3 90.7 - - + +
197A PHE* 1.3 62.8 + - + +
198A LYS 3.4 0.2 - - - -
199A GLN* 3.5 14.7 + - - +
200A LEU* 3.1 30.1 + - + +
451A PHE* 3.5 43.5 - - + -
514A PHE* 4.0 17.0 - - + -
516A PHE* 3.4 36.3 - - + -
517A LEU* 3.8 26.7 - - + -
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Residues in contact with PHE 197 (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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162A THR* 3.9 19.3 - - + -
163A PRO* 3.3 35.2 - - + -
165A LEU 5.9 0.2 - - - -
166A THR* 3.6 22.2 - - - -
167A LYS 5.9 0.4 - - - -
194A PRO* 3.1 12.9 + - + +
196A LEU* 1.3 79.2 - - + +
198A LYS* 1.3 59.1 + - - +
200A LEU* 3.4 8.3 + - + +
201A LEU* 3.1 31.3 + - - +
554B PHE* 3.5 42.0 - + + -
556B LYS* 6.4 0.2 - - - -
562B CYS* 5.0 5.4 - - - -
564B MET* 3.8 19.7 - - + -
565B THR* 4.0 23.1 - - + -
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Residues in contact with LYS 198 (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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162A THR* 5.0 0.6 - - - +
194A PRO* 2.8 21.2 + - - +
195A GLN* 3.6 16.1 - - - +
197A PHE* 1.3 70.3 - - - +
199A GLN* 1.3 68.9 + - + +
201A LEU* 3.1 20.8 + - - +
202A MET* 3.2 19.6 + - - +
209A TYR* 3.6 30.1 - - + -
233A ASP* 2.6 39.6 + - - +
234A VAL 3.1 14.3 + - - +
235A GLU* 2.9 28.2 - - + +
489A ARG* 3.4 17.6 - - - +
531A LEU 4.2 6.7 + - - +
532A ALA* 4.8 2.4 - - - +
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Residues in contact with GLN 199 (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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195A GLN* 3.6 17.4 + - - +
196A LEU* 3.5 17.1 + - + +
197A PHE 3.3 0.4 - - - -
198A LYS* 1.3 74.5 - - + +
200A LEU* 1.3 66.8 + - - +
201A LEU 3.0 1.6 - - - -
202A MET* 2.9 14.8 + - - +
203A MET* 3.0 27.6 + - + +
235A GLU* 4.0 11.9 - - - +
449A HIS* 4.3 4.4 + - - -
451A PHE* 3.7 32.7 - - - +
489A ARG* 3.4 30.5 - - - +
490A ILE 4.9 2.4 - - - +
517A LEU* 5.3 3.8 - - + +
528A HIS* 3.3 32.7 + - + +
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Residues in contact with LEU 200 (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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196A LEU 3.1 18.3 + - - +
197A PHE* 3.4 16.2 - - + +
199A GLN* 1.3 77.2 - - - +
201A LEU* 1.3 57.4 + - - +
203A MET* 3.2 22.7 + - + +
204A SER* 3.0 29.7 + - - -
516A PHE* 3.5 33.2 - - + -
517A LEU* 4.5 10.1 - - + -
520A ALA* 4.2 20.0 - - + -
126B TYR* 3.9 17.7 - - + +
554B PHE* 4.1 9.9 - - + -
564B MET* 3.6 24.9 - - + -
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Residues in contact with LEU 201 (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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160A ILE* 3.8 24.9 - - + -
162A THR* 4.4 5.4 - - + -
197A PHE 3.1 19.2 + - - +
198A LYS* 3.4 11.4 - - - +
199A GLN 3.0 1.0 - - - -
200A LEU* 1.3 75.2 - - - +
202A MET* 1.3 71.0 + - + +
203A MET 3.1 1.8 - - - -
204A SER* 3.2 11.0 + - - -
205A GLY 3.5 0.2 + - - -
206A PHE* 3.4 50.3 + - + +
209A TYR* 3.8 24.2 - - + -
129B LEU* 4.3 4.0 - - + -
553B ALA* 4.1 11.0 - - + -
554B PHE* 3.3 27.8 - - + -
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Residues in contact with MET 202 (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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198A LYS 3.2 5.4 + - - +
199A GLN 2.9 7.9 + - - +
201A LEU* 1.3 83.2 - - + +
203A MET* 1.3 61.2 + - + +
204A SER 3.5 0.2 + - - -
205A GLY 3.6 6.8 + - - -
206A PHE* 3.5 25.3 - - + +
207A ASP 3.5 17.5 - - - +
208A ARG 4.2 0.2 - - - -
209A TYR* 3.8 28.0 - - + +
235A GLU* 3.2 39.5 - - + +
236A THR 3.7 4.0 - - - -
237A SER* 3.3 24.0 + - - +
526A PRO* 3.5 18.4 - - + +
528A HIS* 4.1 21.8 - - + -
23B TRP* 4.1 5.0 - - - -
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Residues in contact with MET 203 (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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199A GLN* 3.0 36.0 + - + +
200A LEU* 3.2 12.8 + - + +
202A MET* 1.3 81.9 - - + +
204A SER* 1.3 57.0 + - - +
205A GLY 3.2 3.4 + - - -
517A LEU* 4.0 22.2 - - + -
520A ALA* 4.0 32.5 - - + +
521A LEU* 4.3 8.5 - - + -
525A THR* 4.2 23.3 - - - +
526A PRO* 4.3 10.5 - - + -
528A HIS* 4.0 13.5 - - - +
23B TRP* 5.0 4.1 + - - -
126B TYR* 4.3 7.2 - - + -
130B ARG* 2.9 40.2 + - - +
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Residues in contact with SER 204 (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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200A LEU 3.0 20.7 + - - -
201A LEU* 3.6 9.3 - - - -
202A MET 3.2 1.0 - - - -
203A MET* 1.3 76.7 - - - +
205A GLY* 1.3 58.6 + - - +
206A PHE* 3.4 12.6 + - - -
126B TYR* 3.1 30.9 - - - -
129B LEU* 3.4 38.7 - - - +
130B ARG* 3.3 17.3 - - - +
135B ALA* 5.6 1.0 - - - +
554B PHE* 4.8 0.7 - - - -
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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