Contacts of the strand formed by residues 319 - 328 (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 LEU 319 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153D GLY* 3.3 30.5 - - - +
154D THR* 4.2 2.7 - - + -
156D ALA* 3.9 14.6 - - + -
157D VAL* 3.7 25.8 - - + -
161D THR* 5.7 0.7 - - + -
163D LEU 3.6 1.6 + - - -
164D VAL* 3.4 21.8 - - + -
165D LEU 2.7 32.8 + - - +
285D ASP* 5.1 8.5 - - - +
299D PHE* 5.7 0.9 - - - -
317D VAL* 3.3 7.3 - - - +
318D ALA* 1.3 83.6 - - + +
320D ALA* 1.3 56.4 + - - +
321D LEU* 3.6 37.7 - - + -
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Residues in contact with ALA 320 (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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165D LEU* 3.5 19.1 - - + -
285D ASP* 3.7 10.8 + - - +
286D LEU* 3.2 36.0 + - + +
287D ARG* 4.8 0.4 - - - +
290D LEU* 4.9 3.6 - - + -
298D MET* 5.3 2.0 - - + -
299D PHE* 3.9 27.2 - - + -
317D VAL* 4.1 6.9 - - + +
319D LEU* 1.3 74.1 - - - +
321D LEU* 1.3 64.5 + - - +
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Residues in contact with LEU 321 (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* 4.0 26.7 - - + -
153D GLY* 3.9 26.0 - - - -
154D THR* 4.2 3.8 - - + +
165D LEU* 3.1 11.1 + - - +
166D VAL* 3.7 12.1 - - + -
167D ASN* 3.2 22.4 + - - +
283D GLU* 4.1 14.1 - - + +
284D VAL 3.5 10.3 - - - +
285D ASP* 4.5 10.3 - - + +
286D LEU* 3.8 8.9 - - - +
319D LEU* 3.6 43.3 - - + -
320D ALA* 1.3 80.3 - - - +
322D GLN* 1.3 65.0 + - - +
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Residues in contact with GLN 322 (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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34D PHE* 3.6 16.3 - - - -
35D SER* 3.1 35.5 + - - +
39D VAL* 3.5 17.2 - - - +
151D LEU* 6.5 0.2 - - - -
167D ASN* 3.0 38.4 + - - +
169D LEU* 4.2 0.4 - - + -
282D THR 3.6 1.6 - - - +
283D GLU* 3.2 3.6 - - - +
284D VAL* 2.7 42.7 + - + +
286D LEU* 4.2 14.8 - - + -
321D LEU* 1.3 78.6 - - - +
323D LYS* 1.3 61.1 + - - +
324D VAL* 2.9 29.2 - - + +
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Residues in contact with LYS 323 (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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148D ILE* 3.5 17.5 - - + -
150D HIS* 3.4 27.4 - - - +
151D LEU* 3.6 18.8 - - + +
152D LEU* 5.6 0.9 - - - +
167D ASN 3.0 5.9 + - - +
168D ALA* 3.2 7.0 - - + +
169D LEU 3.1 22.5 + - - +
281D GLU* 3.3 26.8 + - - +
282D THR 3.4 10.7 - - - +
283D GLU* 3.8 24.9 - - + +
321D LEU* 5.5 0.2 - - - +
322D GLN* 1.3 73.4 - - - +
324D VAL* 1.3 69.4 + - - +
325D LYS* 3.4 29.3 - - - +
1002D CL 3.5 7.6 - - - +
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Residues in contact with VAL 324 (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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33D VAL* 3.3 16.2 - - + +
34D PHE* 4.3 3.4 - - - +
35D SER* 4.0 13.5 - - - +
169D LEU* 3.2 13.9 - - + +
281D GLU* 3.1 5.2 - - - +
282D THR* 3.0 32.3 + - - +
322D GLN* 2.9 33.0 - - - +
323D LYS* 1.3 80.8 - - - +
325D LYS* 1.3 63.8 + - - +
326D ILE* 3.7 28.5 - - + -
372D PHE* 3.9 16.2 - - + -
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Residues in contact with LYS 325 (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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147D MET* 2.6 32.1 + - + +
148D ILE* 3.7 15.7 - - + +
169D LEU 3.0 6.9 + - - +
170D TYR* 3.1 26.1 - - + -
171D PHE 2.7 31.1 + - - -
280D LEU 3.5 4.3 - - - +
281D GLU* 3.9 23.0 + - + -
323D LYS* 3.4 12.8 - - - +
324D VAL* 1.3 73.7 - - - +
326D ILE* 1.3 56.9 + - - +
327D GLU* 5.8 1.1 - - + -
1002D CL 3.0 29.5 - - - +
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Residues in contact with ILE 326 (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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33D VAL* 3.7 26.2 - - + -
34D PHE 4.4 2.9 - - - +
171D PHE* 3.5 19.7 - - + -
235D MET* 5.3 0.9 - - + -
278D PHE* 3.9 12.0 - - + +
279D SER* 3.5 0.5 - - - -
280D LEU 2.8 39.0 + - - +
324D VAL* 3.7 11.2 - - + -
325D LYS* 1.3 78.2 - - - +
327D GLU* 1.3 76.4 + - - +
328D VAL* 4.8 3.4 - - + -
360D PHE* 3.9 25.8 - - + -
372D PHE* 3.6 39.7 - - + -
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Residues in contact with GLU 327 (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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147D MET* 5.7 1.0 - - - +
170D TYR* 2.6 34.3 + - + +
171D PHE* 2.9 15.7 + - - +
172D ASN* 3.5 33.9 + - - +
173D GLY 4.5 2.9 + - - +
228D TYR* 5.0 0.5 + - - -
278D PHE 3.4 3.6 - - - -
279D SER* 2.8 30.2 + - - +
325D LYS* 5.8 1.1 - - + -
326D ILE* 1.3 83.7 - - - +
328D VAL* 1.3 71.3 + - - +
329D ASN* 4.2 9.0 + - - +
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Residues in contact with VAL 328 (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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171D PHE* 5.9 0.2 - - + -
175D TRP* 4.0 13.0 - - + -
202D MET* 3.6 22.7 - - + -
228D TYR* 4.4 6.3 - - - +
235D MET* 3.5 25.1 - - + -
275D LEU* 4.3 5.4 - - + -
276D PRO 4.3 2.5 - - - +
277D LYS* 3.3 5.7 - - - +
278D PHE* 2.7 78.8 + - + +
279D SER* 4.9 1.2 + - - -
326D ILE* 4.8 2.2 - - + -
327D GLU* 1.3 80.2 - - - +
329D ASN* 1.3 66.8 + - - +
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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