Contacts of the strand formed by residues 319 - 328 (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 LEU 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A GLY* 2.9 37.0 - - - +
154A THR* 4.0 8.5 - - + +
156A ALA* 4.4 14.4 - - + -
157A VAL* 4.2 14.1 - - + -
163A LEU 3.6 2.6 + - - -
164A VAL* 3.4 16.8 - - + +
165A LEU 2.6 35.9 + - - +
285A ASP* 4.8 18.4 - - - +
299A PHE* 5.3 1.3 - - - -
317A VAL* 3.3 4.3 - - - -
318A ALA* 1.3 87.0 - - + +
320A ALA* 1.3 57.5 + - - +
321A LEU* 3.9 21.8 - - + -
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Residues in contact with ALA 320 (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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46A LEU* 6.1 2.2 - - + -
165A LEU* 3.6 19.7 - - + -
285A ASP* 3.5 11.2 + - - +
286A LEU* 3.1 28.8 + - + -
290A LEU* 4.3 5.2 - - + -
299A PHE* 3.6 32.8 - - + -
317A VAL* 3.9 9.1 - - + +
319A LEU* 1.3 73.0 - - - +
321A LEU* 1.3 63.0 + - - +
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Residues in contact with LEU 321 (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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151A LEU* 3.5 36.6 - - + -
153A GLY* 3.8 30.5 - - - +
154A THR* 4.5 2.0 - - + +
165A LEU* 3.2 17.3 + - - +
166A VAL* 3.7 17.1 - - + -
167A ASN* 3.2 22.0 + - - +
283A GLU* 3.9 8.5 - - - +
284A VAL 3.1 17.3 - - - +
285A ASP* 4.4 2.7 - - + -
286A LEU* 3.8 7.7 - - - +
319A LEU* 3.9 22.9 - - + -
320A ALA* 1.3 75.6 - - - +
322A GLN* 1.3 69.1 + - - +
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Residues in contact with GLN 322 (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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34A PHE* 3.4 17.3 - - + -
35A SER* 3.0 22.2 + - - -
39A VAL* 3.2 29.3 - - - +
167A ASN* 3.0 36.6 + - - +
169A LEU* 4.9 0.7 - - + -
282A THR 4.0 0.4 - - - +
283A GLU* 3.2 6.1 - - - +
284A VAL* 2.7 36.3 + - + +
286A LEU* 4.1 16.3 - - + +
321A LEU* 1.3 82.2 - - - +
323A LYS* 1.3 64.0 + - - +
324A VAL* 2.9 30.2 - - + +
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Residues in contact with LYS 323 (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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148A ILE* 3.3 26.4 - - + +
150A HIS* 3.3 16.0 + - - +
151A LEU* 3.8 15.3 - - + +
152A LEU* 6.2 0.4 - - - -
167A ASN 2.9 8.2 + - - +
168A ALA* 3.2 5.6 - - + -
169A LEU 3.0 25.5 + - - +
281A GLU* 4.1 15.8 + - + -
282A THR 3.4 5.6 - - - +
283A GLU* 3.6 38.1 - - + -
322A GLN* 1.3 73.1 - - - +
324A VAL* 1.3 67.2 + - - +
325A LYS* 3.7 12.3 - - + +
1001A CL 2.7 32.3 - - - +
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Residues in contact with VAL 324 (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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33A VAL* 3.4 18.3 - - + +
34A PHE* 4.0 6.5 - - + +
35A SER* 3.7 16.4 - - - +
148A ILE* 4.8 0.4 - - - -
169A LEU* 3.5 6.5 - - + +
281A GLU* 3.4 2.3 - - - +
282A THR 2.9 34.9 + - - +
322A GLN* 2.9 32.7 - - + +
323A LYS* 1.3 79.1 - - - +
325A LYS* 1.3 64.0 + - - +
326A ILE* 3.5 32.5 - - + -
372A PHE* 3.8 14.8 - - + -
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Residues in contact with LYS 325 (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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147A MET 3.4 16.7 + - - +
148A ILE* 3.6 19.5 - - + +
169A LEU 3.0 11.7 + - - +
170A TYR* 3.4 17.7 - - + -
171A PHE 2.8 27.5 + - - +
280A LEU 3.7 2.0 - - - -
281A GLU* 3.9 27.6 + - + -
323A LYS* 3.7 9.6 - - + +
324A VAL* 1.3 72.6 - - - +
326A ILE* 1.3 62.2 - - - +
1001A CL 2.9 33.7 - - - +
347D MET* 3.5 32.1 - - + -
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Residues in contact with ILE 326 (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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33A VAL* 3.6 33.7 - - + -
34A PHE 5.3 0.4 - - - +
171A PHE* 3.6 24.9 - - + +
235A MET* 5.0 0.4 - - + -
278A PHE* 4.0 13.6 - - + +
279A SER* 3.2 2.4 - - - -
280A LEU 2.7 41.3 + - - +
324A VAL* 3.5 11.4 - - + -
325A LYS* 1.3 74.6 - - - +
327A GLU* 1.3 71.6 + - - +
328A VAL* 4.5 3.4 - - + -
360A PHE* 3.9 25.6 - - + -
372A PHE* 3.3 38.4 - - + -
347D MET* 3.6 0.2 - - - +
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Residues in contact with GLU 327 (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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170A TYR* 2.7 33.3 + - + +
171A PHE* 2.9 17.6 + - - +
172A ASN* 3.6 27.8 + - - +
173A GLY 3.9 7.6 + - - -
278A PHE 3.4 4.3 - - - -
279A SER* 2.9 24.7 + - - +
326A ILE* 1.3 76.0 - - - +
328A VAL* 1.3 69.2 + - - +
329A ASN* 4.4 6.3 - - - +
347D MET* 3.3 31.1 - - + +
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Residues in contact with VAL 328 (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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172A ASN* 4.9 0.4 - - - +
173A GLY* 5.6 1.8 - - - +
175A TRP* 3.6 24.0 - - + -
202A MET* 3.9 15.5 - - + -
228A TYR* 4.7 4.7 - - - +
235A MET* 3.5 23.3 - - + -
275A LEU* 4.6 3.6 - - + -
276A PRO 4.5 0.4 - - - +
277A LYS* 3.4 5.5 - - - +
278A PHE* 2.6 78.5 + - + +
279A SER* 4.5 1.8 + - - -
326A ILE* 4.5 2.2 - - + -
327A GLU* 1.3 81.5 - - - +
329A ASN* 1.3 67.1 + - - +
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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