Contacts of the strand formed by residues 278 - 285 (chain B) 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 PHE 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235B MET* 4.7 6.7 - - + -
237B ILE* 6.4 0.2 - - + -
275B LEU* 5.6 2.9 - - + -
276B PRO 3.4 12.8 - - - -
277B LYS* 1.3 75.0 - - - +
279B SER* 1.3 60.9 + - - +
280B LEU* 3.4 30.5 - - + -
326B ILE* 4.1 13.5 - - + -
328B VAL* 3.0 65.6 + - + +
358B PHE* 3.6 30.1 - + - -
360B PHE* 3.7 44.6 - + - -
376B VAL* 4.2 5.6 - - + -
379B PRO* 4.0 21.5 - - + +
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 1.3 75.0 - - - +
280B LEU* 1.3 68.7 + - - +
325B LYS* 5.9 1.4 - - - +
326B ILE 3.4 7.1 + - - -
327B GLU* 3.5 26.5 + - - +
379B PRO* 4.8 3.9 + - - +
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASN* 3.4 46.0 - - + +
32B VAL 4.2 1.6 - - - +
33B VAL* 3.2 30.5 - - + -
278B PHE* 3.4 30.3 - - + -
279B SER* 1.3 84.1 + - - +
281B GLU* 1.3 63.4 + - - +
282B THR* 5.4 1.1 - - + -
325B LYS* 3.6 3.5 - - - +
326B ILE* 2.9 37.8 + - + +
360B PHE* 4.5 1.6 - - + -
375B GLN 3.8 14.8 - - - +
376B VAL* 4.1 11.4 - - + -
378B GLU 4.8 1.1 - - - +
379B PRO* 5.2 2.0 - - + +
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B HIS* 5.3 1.2 - - - -
280B LEU* 1.3 80.2 - - - +
282B THR* 1.3 69.2 + - - +
323B LYS* 3.2 32.7 + - - -
324B VAL 3.3 12.3 - - - +
325B LYS* 3.1 37.7 + - + -
1004B CL 4.1 1.7 - - - +
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Residues in contact with THR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASN* 4.9 4.0 - - + +
32B VAL* 3.9 11.5 - - - +
33B VAL* 3.0 53.4 + - + +
280B LEU* 5.4 0.9 - - + -
281B GLU* 1.3 80.7 - - - +
283B GLU* 1.3 61.7 + - - +
284B VAL* 3.5 18.2 - - - +
322B GLN 3.6 0.7 - - - +
323B LYS* 3.2 7.0 - - - +
324B VAL* 2.9 32.8 + - - +
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LEU* 3.3 16.3 - - + -
152B LEU* 2.9 34.0 + - + +
153B GLY* 2.9 30.5 + - - -
282B THR* 1.3 77.3 + - - +
284B VAL* 1.3 64.7 + - - +
285B ASP 4.3 0.2 + - - -
321B LEU* 3.6 19.7 - - + +
322B GLN 3.0 10.3 - - - +
323B LYS* 4.0 21.9 + - + +
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL* 4.6 25.1 - - + -
33B VAL 4.8 1.1 - - - +
34B PHE* 4.1 28.0 - - + -
282B THR* 3.5 21.1 - - - +
283B GLU* 1.3 74.1 - - - +
285B ASP* 1.3 73.2 + - - +
286B LEU* 3.3 18.8 + - + +
289B PRO* 4.8 4.5 - - + -
321B LEU* 3.2 10.8 - - - +
322B GLN* 2.7 38.9 + - + +
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Residues in contact with ASP 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B GLU 4.3 1.0 + - - -
284B VAL* 1.3 77.3 - - - +
286B LEU* 1.3 60.2 + - - +
287B ARG* 3.0 26.6 + - - +
288B LYS 4.5 1.0 + - - -
289B PRO* 3.8 9.4 - - - +
299B PHE* 5.8 0.2 - - - -
319B LEU* 4.5 11.5 - - - +
320B ALA* 3.5 14.9 + - - +
321B LEU* 4.1 12.1 - - + +
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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