Contacts of the strand formed by residues 267 - 276 (chain A) in PDB entry 1DVM
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 THR 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A PHE 3.4 0.7 - - - +
209A ASN* 3.4 6.7 - - - -
210A TYR* 2.6 43.1 + - - +
265A ASN 4.0 5.7 + - - -
266A MET* 1.3 79.9 + - - +
268A ARG* 1.3 65.0 + - - +
269A LEU* 3.6 22.8 + - + +
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Residues in contact with ARG 268 (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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176A LYS* 5.0 11.5 - - - +
207A LYS* 4.0 32.5 + - + +
208A PHE 3.0 10.3 - - - +
209A ASN* 3.3 28.7 + - - +
267A THR* 1.3 79.1 - - - +
269A LEU* 1.3 65.8 + - - +
270A PRO* 4.2 4.0 - - - +
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Residues in contact with LEU 269 (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 LYS* 4.2 1.3 - - - -
208A PHE* 2.8 28.9 + - - +
210A TYR* 3.4 37.9 - - + -
267A THR* 4.0 25.6 - - + +
268A ARG* 1.3 80.4 - - - +
270A PRO* 1.3 65.5 - - + +
271A ARG* 3.2 51.0 + - + +
352A ILE* 6.3 0.2 - - + -
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Residues in contact with PRO 270 (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 ASN 3.3 11.0 - - - +
207A LYS* 4.0 23.6 - - + -
268A ARG 4.2 2.7 - - - +
269A LEU* 1.3 83.1 - - + +
271A ARG* 1.3 70.0 + - - +
347A MET 5.9 0.4 - - - +
348A ALA* 3.8 6.5 - - + -
349A PRO* 2.9 45.4 - - + +
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Residues in contact with ARG 271 (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 GLN 3.6 2.3 - - - +
205A THR* 3.1 2.1 - - - -
206A ASN 3.0 31.3 + - - +
208A PHE* 3.7 15.3 - - + -
210A TYR* 6.2 0.9 - - + -
224A LEU* 6.1 0.9 - - + -
269A LEU* 3.2 55.1 + - + +
270A PRO* 1.3 95.5 + - - +
272A LEU* 1.3 64.8 + - - +
273A LEU 3.7 0.7 - - - -
348A ALA* 3.5 7.1 - - - +
349A PRO* 4.2 11.6 - - - +
350A GLU* 3.1 42.9 - - - +
351A GLU 4.2 0.9 - - - +
352A ILE* 4.3 30.5 - - + +
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Residues in contact with LEU 272 (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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203A ALA* 4.4 11.4 - - + -
204A GLN* 3.5 20.4 - - - +
205A THR* 3.4 28.0 - - + +
271A ARG* 1.3 72.3 - - - +
273A LEU* 1.3 60.7 + - - +
274A VAL* 3.8 11.6 + - + +
348A ALA* 3.8 3.8 - - + +
350A GLU 3.0 6.9 + - - +
351A GLU* 3.2 30.9 - - + +
352A ILE 2.9 22.8 + - - +
353A ILE* 5.2 0.4 - - + -
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Residues in contact with LEU 273 (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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179A PHE* 3.9 13.0 - - + -
202A MET 3.7 0.2 - - - +
203A ALA* 3.0 5.0 - - - +
204A GLN 2.7 38.3 + - - +
208A PHE* 3.4 42.8 - - + -
224A LEU* 3.8 25.6 - - + -
226A LEU* 3.9 31.0 - - + -
237A ILE* 5.1 1.1 - - + -
271A ARG* 3.7 1.6 - - + -
272A LEU* 1.3 73.5 - - - +
274A VAL* 1.3 69.9 + - - +
275A LEU* 4.0 9.2 - - + -
352A ILE* 3.3 22.4 - - + +
354A ILE* 4.3 8.1 - - + -
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Residues in contact with VAL 274 (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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185A HIS* 4.2 6.3 - - + -
187A ARG* 3.3 30.7 - - - +
201A MET* 3.8 30.7 - - + -
202A MET 3.1 4.9 - - - +
203A ALA* 4.0 14.8 - - + -
272A LEU* 3.8 13.9 + - + -
273A LEU* 1.3 77.3 - - - +
275A LEU* 1.3 60.1 + - - +
276A PRO* 4.4 0.3 - - - +
352A ILE 3.0 6.5 + - - -
353A ILE* 3.5 25.4 - - + -
354A ILE* 3.0 33.4 + - - +
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Residues in contact with LEU 275 (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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175A TRP* 4.7 2.0 - - + -
179A PHE* 3.8 7.9 - - + -
201A MET* 3.9 2.9 - - - -
202A MET* 2.6 64.1 + - + +
226A LEU* 3.5 30.5 - - + -
235A MET* 5.7 1.1 - - - -
237A ILE* 3.2 26.0 - - + -
273A LEU* 4.0 10.7 - - + -
274A VAL* 1.3 74.5 - - - +
276A PRO* 1.3 84.2 - - + +
277A LYS 3.4 0.2 + - - -
278A PHE* 5.2 2.5 - - + -
328A VAL* 4.6 10.3 - - + -
354A ILE* 3.9 15.5 - - + -
358A PHE* 4.5 8.7 - - + -
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Residues in contact with PRO 276 (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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189A PHE* 3.6 20.0 - - + -
199A VAL* 4.7 1.6 - - + -
200A PRO 3.6 2.5 - - - +
201A MET* 3.6 20.4 - - + -
202A MET* 4.2 1.7 - - - +
275A LEU* 1.3 103.5 - - + +
277A LYS* 1.3 59.8 + - - +
278A PHE* 3.3 18.0 - - + -
354A ILE* 3.1 33.2 - - + +
358A PHE* 4.2 7.6 - - + -
379A PRO* 3.9 24.9 - - + -
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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