Contacts of the strand formed by residues 319 - 328 (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 LEU 319 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B GLY* 3.1 35.0 - - - +
154B THR* 4.1 1.6 - - + +
156B ALA* 4.7 13.2 - - + -
157B VAL* 4.1 20.4 - - + +
161B THR* 5.7 1.8 - - + -
163B LEU 3.3 3.0 + - - -
164B VAL* 3.3 19.3 - - + +
165B LEU* 2.6 35.4 + - - +
285B ASP* 4.5 13.2 - - - +
317B VAL* 3.4 4.4 - - - +
318B ALA* 1.3 86.7 - - + +
320B ALA* 1.3 56.8 + - - +
321B LEU* 3.8 32.3 - - + -
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Residues in contact with ALA 320 (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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165B LEU* 3.4 20.4 - - + -
285B ASP* 3.5 11.5 + - - +
286B LEU* 2.9 42.4 + - + +
287B ARG 5.0 0.2 - - - +
290B LEU* 5.0 3.4 - - + -
299B PHE* 4.0 17.8 - - + -
317B VAL* 3.9 17.0 - - + +
319B LEU* 1.3 75.5 - - - +
321B LEU* 1.3 60.6 + - - +
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Residues in contact with LEU 321 (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* 3.6 32.3 - - + -
153B GLY* 3.6 22.7 - - - +
154B THR* 4.1 1.3 - - - +
165B LEU* 2.9 14.2 + - - +
166B VAL* 3.6 6.4 - - + +
167B ASN* 3.0 26.9 + - - +
283B GLU* 3.6 26.7 - - + +
284B VAL 3.2 15.7 - - - +
285B ASP* 4.1 12.8 - - + +
286B LEU* 4.4 3.8 - - - +
319B LEU* 3.8 35.7 - - + -
320B ALA* 1.3 75.6 - - - +
322B GLN* 1.3 60.8 + - - +
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Residues in contact with GLN 322 (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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34B PHE* 3.2 18.9 - - - -
35B SER* 3.1 33.1 + - - -
38B GLY* 4.0 0.4 - - - -
39B VAL* 3.0 31.5 - - - +
167B ASN* 2.7 33.5 + - + +
282B THR 3.6 1.4 - - - +
283B GLU* 3.0 5.2 - - - -
284B VAL* 2.7 44.0 + - + +
286B LEU* 4.2 15.3 - - + -
321B LEU* 1.3 75.8 - - - +
323B LYS* 1.3 62.9 + - - +
324B VAL* 3.6 16.0 - - + +
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Residues in contact with LYS 323 (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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148B ILE* 3.5 26.4 - - + +
150B HIS* 2.8 43.4 + - - +
151B LEU* 4.3 15.8 - - + +
152B LEU* 5.5 3.2 - - - +
167B ASN 2.8 10.8 + - - +
168B ALA* 3.2 5.9 - - + -
169B LEU 3.1 23.7 + - - -
281B GLU* 3.2 34.5 + - - -
282B THR 3.2 9.2 - - - +
283B GLU* 4.0 22.6 + - + +
321B LEU 4.3 0.2 - - - -
322B GLN* 1.3 73.9 - - - +
324B VAL* 1.3 65.9 + - - +
325B LYS* 4.7 1.3 - - - +
1004B CL 3.3 15.6 - - - +
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Residues in contact with VAL 324 (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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33B VAL* 3.4 30.4 - - + +
34B PHE* 4.3 3.8 - - - -
35B SER* 3.9 20.4 - - - +
148B ILE* 4.3 0.9 - - - -
169B LEU* 3.3 14.4 - - + +
280B LEU 4.6 0.3 - - - -
281B GLU* 3.3 6.4 - - - +
282B THR* 2.9 33.7 + - - +
322B GLN* 3.6 24.2 - - - +
323B LYS* 1.3 79.7 - - - +
325B LYS* 1.3 66.3 + - - +
372B PHE* 3.3 28.5 - - + -
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Residues in contact with LYS 325 (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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147B MET* 3.0 31.8 + - + +
148B ILE* 3.9 17.9 - - + +
169B LEU 3.2 5.5 + - - +
170B TYR* 3.4 28.7 - - + -
171B PHE* 2.8 27.0 + - - +
279B SER* 5.9 1.3 - - - +
280B LEU 3.6 8.7 - - - +
281B GLU* 3.1 37.3 + - + -
324B VAL* 1.3 77.5 - - - +
326B ILE* 1.3 62.8 + - - +
327B GLU* 3.9 12.3 - - - +
1004B CL 3.6 14.1 - - - +
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Residues in contact with ILE 326 (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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33B VAL* 3.9 33.2 - - + -
171B PHE* 3.2 38.1 - - + +
235B MET* 3.8 16.6 - - + -
278B PHE* 4.1 15.5 - - + -
279B SER* 3.4 3.3 + - - -
280B LEU* 2.9 41.5 + - + +
324B VAL* 4.3 2.4 - - + -
325B LYS* 1.3 74.5 - - - +
327B GLU* 1.3 72.2 - - - +
328B VAL* 5.1 0.7 - - + +
360B PHE* 3.8 22.0 - - + -
362B VAL* 4.3 4.0 - - + -
372B PHE* 4.5 9.0 - - + -
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Residues in contact with GLU 327 (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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147B MET* 5.1 3.6 - - - +
170B TYR* 2.5 42.6 + - - -
171B PHE* 3.0 9.3 + - - +
172B ASN* 3.3 20.9 + - - +
173B GLY* 3.0 26.0 + - - -
228B TYR* 5.6 0.7 + - - -
278B PHE 4.0 2.9 - - - +
279B SER* 3.5 25.4 + - - +
325B LYS* 3.9 14.9 - - - +
326B ILE* 1.3 76.9 - - - +
328B VAL* 1.3 60.0 + - - +
329B ASN* 3.9 4.5 - - + +
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Residues in contact with VAL 328 (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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173B GLY* 5.2 1.1 - - - +
175B TRP* 3.3 35.9 - - + -
202B MET* 3.9 9.6 - - + -
228B TYR* 5.0 1.3 - - - +
235B MET* 4.3 17.7 - - + -
275B LEU* 4.8 4.9 - - + -
276B PRO 4.5 0.4 - - - +
277B LYS* 3.5 11.7 - - - +
278B PHE* 3.0 81.3 + - + +
326B ILE* 4.2 1.1 - - + -
327B GLU* 1.3 72.0 - - - +
329B ASN* 1.3 58.9 + - - +
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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