Contacts of the strand formed by residues 278 - 285 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D VAL* 5.7 0.2 - - + -
235D MET* 4.5 6.3 - - + -
275D LEU* 4.9 4.9 - - + -
276D PRO* 3.4 15.7 - - + -
277D LYS* 1.3 73.9 - - - +
279D SER* 1.3 59.7 + - - +
280D LEU* 4.1 27.4 - - + -
326D ILE* 4.5 8.1 - - + -
327D GLU* 3.4 2.1 - - - -
328D VAL* 2.7 74.3 + - + -
358D PHE* 3.6 31.0 - + - -
360D PHE* 3.9 35.2 - + - -
376D VAL* 4.1 7.2 - - + -
379D PRO* 4.3 19.7 - - + +
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Residues in contact with SER 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D PHE* 1.3 77.4 + - - +
280D LEU* 1.3 68.3 + - - +
281D GLU* 5.7 0.9 - - - +
326D ILE 3.5 6.1 - - - -
327D GLU* 2.8 32.1 + - - +
328D VAL 4.8 1.9 + - - -
329D ASN* 5.2 1.9 + - - -
379D PRO 5.5 1.6 + - - -
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Residues in contact with LEU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ASN* 3.4 49.4 - - + +
32D VAL 5.2 0.2 - - - +
33D VAL* 3.7 26.0 - - + +
278D PHE* 4.0 16.5 - - + -
279D SER* 1.3 89.0 - - - +
281D GLU* 1.3 62.7 + - - +
282D THR* 5.3 0.9 - - + -
324D VAL 3.7 1.2 - - - +
325D LYS* 3.5 1.8 - - - +
326D ILE* 2.8 37.2 + - - +
360D PHE* 5.7 0.2 - - + -
375D GLN 5.7 0.2 - - - -
376D VAL* 4.0 22.2 - - + -
378D GLU 4.6 4.3 - - - +
379D PRO 4.8 8.7 - - - +
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Residues in contact with GLU 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D SER 5.7 0.7 - - - +
280D LEU* 1.3 77.6 - - - +
282D THR* 1.3 68.9 + - - +
323D LYS* 3.3 23.8 + - - +
324D VAL 3.1 9.6 - - - +
325D LYS* 3.9 24.5 + - + -
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Residues in contact with THR 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ASN* 4.2 8.1 - - + +
32D VAL* 3.7 14.7 - - - +
33D VAL* 2.7 52.3 + - + +
280D LEU* 5.3 1.6 - - + -
281D GLU* 1.3 82.9 - - - +
283D GLU* 1.3 62.1 + - - +
284D VAL* 3.9 13.0 - - - +
322D GLN 3.6 2.1 - - - +
323D LYS* 3.4 3.9 - - - +
324D VAL* 3.0 30.2 + - - +
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Residues in contact with GLU 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D LEU* 3.5 10.1 - - - -
152D LEU* 3.1 37.0 + - + +
153D GLY* 2.7 31.2 + - - -
282D THR* 1.3 75.2 - - - +
284D VAL* 1.3 64.5 + - - +
285D ASP 4.3 0.5 + - - -
321D LEU* 4.1 16.3 - - + +
322D GLN 3.2 10.5 - - - +
323D LYS* 3.8 29.1 - - + +
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Residues in contact with VAL 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL* 4.2 34.8 - - + -
32D VAL* 5.3 0.9 - - + -
33D VAL 4.9 0.4 - - - +
34D PHE* 4.2 17.9 - - + -
282D THR* 3.9 19.1 - - - +
283D GLU* 1.3 79.0 - - - +
285D ASP* 1.3 75.3 + - - +
286D LEU* 3.3 19.7 + - + +
289D PRO* 4.6 3.4 - - + -
321D LEU* 3.5 7.0 - - - -
322D GLN* 2.7 39.1 + - + +
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Residues in contact with ASP 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D GLU 4.3 0.6 + - - -
284D VAL* 1.3 72.6 - - - +
286D LEU* 1.3 61.9 + - - +
287D ARG* 2.9 37.7 + - - +
288D LYS 5.4 0.4 - - - -
289D PRO* 3.3 19.8 - - - +
319D LEU* 5.1 8.2 - - - +
320D ALA 3.7 12.1 + - - +
321D LEU* 4.5 9.7 - - + +
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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