Contacts of the helix formed by residues 198 - 215 (chain A) in PDB entry 1LMU
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 VAL 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ARG* 5.6 1.8 - - - +
169A ASP* 5.5 2.7 - - - +
196A GLY 3.3 0.2 - - - -
197A ARG* 1.3 108.9 - - + +
199A GLN* 1.4 62.1 + - - +
200A THR 3.4 0.2 - - - -
201A PRO* 3.4 4.4 - - - +
202A VAL* 2.9 35.5 + - + +
500A MET* 5.5 0.4 - - - -
522A LEU* 4.4 9.4 - - + +
523A GLY* 3.8 29.4 - - - +
527A THR* 5.8 0.2 - - - +
531A ILE* 2.9 35.4 - - + -
571A THR* 5.4 1.1 - - - +
575A GLU* 4.6 1.3 - - + +
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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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194A SER* 2.9 46.2 + - - -
195A VAL 4.0 2.6 - - - +
196A GLY* 3.4 21.5 - - - +
198A VAL* 1.4 75.4 - - - +
200A THR* 1.3 73.1 + - - +
202A VAL* 3.2 3.3 + - - +
203A LEU* 2.9 21.3 + - - +
531A ILE* 3.7 26.6 - - + +
534A LEU* 3.6 24.5 - - + +
535A LEU* 3.8 22.5 - - + +
538A ARG* 5.2 0.4 - - - +
540A PHE* 5.2 2.6 - - - -
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Residues in contact with THR 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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172A TYR* 4.5 0.7 + - - -
194A SER 4.1 6.7 - - - +
195A VAL* 3.5 26.1 - - + +
196A GLY 2.6 36.9 + - - +
199A GLN* 1.3 84.9 - - + +
201A PRO* 1.3 67.0 - - - +
203A LEU* 2.8 10.1 + - + +
204A GLY* 2.7 25.5 + - - -
535A LEU* 6.4 0.2 - - + -
557A LEU* 4.6 12.3 - - + -
558A ILE* 6.0 0.3 - - - +
561A LEU* 4.6 9.0 - - + -
565A ALA* 3.0 19.0 + - - +
566A ALA* 4.4 3.0 - - - +
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Residues in contact with PRO 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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197A ARG 2.8 30.3 - - - +
198A VAL* 3.4 4.0 - - - +
200A THR* 1.3 99.2 - - - +
202A VAL* 1.3 60.8 + - - +
204A GLY* 3.1 1.6 + - - -
205A LEU* 3.0 28.3 + - - +
522A LEU* 4.0 19.7 - - + -
565A ALA 3.5 11.9 - - - +
566A ALA 3.4 18.9 - - - +
567A ARG 3.6 20.9 - - - +
568A PRO* 4.0 4.3 - - + -
571A THR* 5.0 2.0 - - - +
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Residues in contact with VAL 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 VAL* 2.9 33.1 + - + +
199A GLN 3.2 7.2 + - - +
200A THR 3.1 0.6 - - - -
201A PRO* 1.3 77.6 - - - +
203A LEU* 1.3 62.8 + - - +
205A LEU* 3.1 24.0 + - - +
206A VAL* 3.5 7.5 + - + +
496A LEU* 4.3 23.1 - - + -
500A MET* 3.5 38.6 - - + -
522A LEU* 4.6 5.6 - - + -
531A ILE* 4.1 8.1 - - + -
532A ILE* 5.2 2.2 - - + -
535A LEU* 3.8 16.6 - - + -
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Residues in contact with LEU 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 2.9 12.6 + - - +
200A THR* 2.8 14.5 + - + +
202A VAL* 1.3 75.8 - - - +
204A GLY* 1.3 64.3 + - - +
206A VAL* 3.1 7.7 + - - +
207A VAL* 3.0 40.4 + - + -
535A LEU* 4.0 13.5 - - + -
540A PHE* 3.2 40.8 - - + +
541A LEU* 3.5 24.5 - - + -
554A GLY* 3.8 15.3 - - - +
557A LEU* 5.2 7.9 - - + -
558A ILE* 4.3 8.3 - - + -
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Residues in contact with GLY 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 THR 2.7 13.2 + - - -
201A PRO 3.1 5.1 + - - -
203A LEU* 1.3 77.6 - - - +
205A LEU* 1.3 61.9 + - - +
207A VAL* 3.1 0.7 + - - +
208A ARG* 2.9 35.9 + - - +
558A ILE* 3.3 22.2 - - - -
566A ALA* 4.0 11.4 - - - -
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Residues in contact with LEU 205 (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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201A PRO 3.0 20.2 + - - +
202A VAL* 3.1 13.9 + - - +
204A GLY* 1.3 76.3 - - - +
206A VAL* 1.3 62.7 + - - +
208A ARG* 3.5 9.8 + - - +
209A ARG* 3.1 17.8 + - - +
491A PHE* 3.4 22.3 - - + -
496A LEU* 4.5 8.3 - - + -
499A ALA* 3.8 30.1 - - + -
500A MET* 4.6 6.7 - - + +
503A ILE* 4.1 23.8 - - + -
506A PHE* 4.0 31.0 - - + -
522A LEU* 5.1 1.1 - - + -
568A PRO* 5.0 9.0 - - + -
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Residues in contact with VAL 206 (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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202A VAL 3.6 13.5 - - - +
203A LEU 3.1 6.8 + - - +
205A LEU* 1.3 73.7 - - - +
207A VAL* 1.3 64.1 + - - +
209A ARG* 3.5 1.2 + - - +
210A ASP* 3.0 35.1 + - - +
491A PHE* 4.1 13.0 - - + -
496A LEU* 3.9 28.5 - - + -
541A LEU* 3.8 23.3 - - + -
548A ILE* 4.3 12.3 - - + +
549A HIS 4.0 3.4 - - - -
550A SER* 3.0 32.3 - - - +
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 3.0 38.3 + - + +
204A GLY 3.1 0.2 + - - -
206A VAL* 1.3 72.4 - - - +
208A ARG* 1.3 62.8 + - + +
210A ASP* 3.1 3.3 + - - +
211A GLU* 2.8 43.5 + - - +
550A SER* 3.3 18.6 - - - +
554A GLY 4.3 2.5 - - - +
555A LYS* 4.0 12.8 - - + +
558A ILE* 3.2 41.7 - - + -
559A HIS* 4.7 2.7 - - + -
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Residues in contact with ARG 208 (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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204A GLY* 2.9 24.8 + - - +
205A LEU* 4.1 10.8 - - - +
207A VAL* 1.3 76.9 - - + +
209A ARG* 1.3 59.8 + - - +
211A GLU* 3.1 8.0 + - - +
212A GLU* 2.8 29.3 + - - +
558A ILE* 5.1 6.2 - - + +
563A GLU* 4.1 16.2 + - - -
566A ALA* 3.4 37.8 + - - +
567A ARG* 3.2 62.5 - - - +
568A PRO* 5.0 2.6 - - - +
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Residues in contact with ARG 209 (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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205A LEU 3.1 10.0 + - - +
206A VAL 3.7 2.5 - - - +
207A VAL 3.2 0.2 - - - -
208A ARG* 1.3 77.4 - - - +
210A ASP* 1.3 74.7 + - - +
212A GLU* 3.1 17.4 + - - +
213A ILE* 2.9 29.4 + - + +
488A PRO* 4.8 12.0 - - + +
489A ARG* 2.7 35.3 + - - +
490A HIS* 3.7 6.4 + - - +
491A PHE* 2.9 76.0 - - + +
495A THR* 4.2 9.1 + - - +
506A PHE* 5.3 7.1 - - - -
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Residues in contact with ASP 210 (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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206A VAL* 3.0 21.8 + - - +
207A VAL 3.5 0.7 - - - +
209A ARG* 1.3 81.7 - - - +
211A GLU* 1.3 60.8 + - - +
213A ILE* 3.3 4.3 + - - +
214A GLU* 3.0 22.4 + - - +
490A HIS* 2.7 38.4 + - + -
548A ILE 4.6 0.7 - - - +
549A HIS* 3.6 5.9 - - - +
550A SER* 2.8 34.2 + - - +
555A LYS* 3.3 23.4 + - - +
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Residues in contact with GLU 211 (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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207A VAL* 2.8 29.9 + - + +
208A ARG* 3.5 11.7 - - - +
210A ASP* 1.3 74.5 - - - +
212A GLU* 1.3 64.4 + - - +
214A GLU* 3.0 9.1 + - + +
215A ASN* 3.0 38.8 + - - +
555A LYS* 3.9 14.7 - - - +
559A HIS* 3.6 25.0 + - - -
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Residues in contact with GLU 212 (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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208A ARG 2.8 16.3 + - - +
209A ARG* 3.1 17.9 + - - +
211A GLU* 1.3 77.5 - - - +
213A ILE* 1.3 62.6 + - + +
215A ASN* 3.4 10.9 + - - +
216A PHE* 3.4 17.2 + - + +
488A PRO* 3.6 28.6 - - + +
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Residues in contact with ILE 213 (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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209A ARG* 2.9 20.8 + - - +
210A ASP 3.6 6.1 - - - +
212A GLU* 1.3 76.6 - - - +
214A GLU* 1.3 63.1 + - - +
216A PHE* 3.2 20.9 + - - +
487A PRO* 4.4 11.5 - - + +
488A PRO* 3.3 38.8 - - + +
489A ARG 3.9 3.1 - - - +
490A HIS* 3.3 58.1 - - + +
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Residues in contact with GLU 214 (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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210A ASP 3.0 13.2 + - - +
211A GLU* 3.0 12.7 + - + +
213A ILE* 1.3 79.5 - - - +
215A ASN* 1.4 89.7 + - - +
216A PHE 3.2 6.2 + - - +
555A LYS* 6.6 0.2 - - - -
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Residues in contact with ASN 215 (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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211A GLU* 3.0 30.2 + - - +
212A GLU* 3.6 6.0 - - - +
214A GLU* 1.4 103.0 + - - +
216A PHE* 1.3 58.2 + - - +
217A VAL* 3.8 3.6 + - - +
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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