Contacts of the helix formed by residues 255 - 265 (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 SER 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B ASP* 4.9 7.2 - - - -
17B VAL* 4.1 12.2 - - - +
253B ILE 3.4 5.5 + - - -
254B LEU* 1.3 77.4 - - - +
256B ALA* 1.3 65.3 + - - +
257B GLN* 4.0 5.8 - - - +
258B LEU* 2.8 38.9 + - - +
259B ILE* 3.1 22.0 + - - +
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Residues in contact with ALA 256 (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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10B HIS* 3.6 28.7 - - + +
13B SER* 4.2 9.9 - - - -
14B ASP* 3.8 34.1 + - - +
17B VAL* 4.6 8.9 - - - +
255B SER* 1.3 73.2 - - - +
257B GLN* 1.3 61.4 + - - +
259B ILE* 3.8 8.2 - - - +
260B SER* 3.7 20.1 + - - -
368B GLY 5.5 3.2 - - - +
370B VAL* 4.9 5.5 - - + +
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Residues in contact with GLN 257 (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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10B HIS* 3.4 29.3 + - + -
14B ASP* 5.7 1.8 - - - +
255B SER* 3.2 6.1 + - - +
256B ALA* 1.3 77.2 - - + +
258B LEU* 1.3 64.3 + - - +
260B SER* 3.2 7.9 + - - +
261B HIS* 3.0 23.7 + - - +
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Residues in contact with LEU 258 (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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213B PHE* 4.0 12.3 - - + -
221B TYR* 3.5 9.2 - - - +
253B ILE* 3.0 43.5 - - + +
254B LEU* 3.7 8.1 - - - -
255B SER* 2.8 24.4 + - - +
257B GLN* 1.3 75.8 - - - +
259B ILE* 1.3 51.9 + - - +
261B HIS* 3.0 11.7 + - - +
262B TRP* 2.7 79.1 + - + +
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Residues in contact with ILE 259 (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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17B VAL* 5.9 2.9 - - + -
236B PHE* 4.4 8.7 - - + -
254B LEU* 5.0 3.8 - - + -
255B SER 3.1 19.5 + - - +
256B ALA* 3.8 10.5 - - - +
257B GLN 3.3 0.6 - - - -
258B LEU* 1.3 75.4 - - + +
260B SER* 1.3 65.0 + - - +
262B TRP* 3.4 38.2 - - + +
263B LYS* 3.4 18.9 + - - +
361B VAL* 4.1 29.6 - - + -
363B ARG* 3.4 40.8 + - + +
368B GLY 5.6 1.6 - - - +
370B VAL* 4.6 13.9 - - + -
373B MET* 6.3 1.8 - - + -
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Residues in contact with SER 260 (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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256B ALA 3.7 11.6 + - - -
257B GLN* 3.2 9.7 + - - -
258B LEU 3.2 0.4 - - - -
259B ILE* 1.3 79.2 - - - +
261B HIS* 1.3 61.3 + - - +
263B LYS* 3.1 10.2 + - - +
264B GLY* 2.9 24.1 + - - -
363B ARG* 3.4 24.3 + - - +
368B GLY* 5.1 4.3 + - - -
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Residues in contact with HIS 261 (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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213B PHE* 3.2 26.8 - + - -
257B GLN 3.0 12.9 + - - +
258B LEU* 3.2 14.1 - - - +
260B SER* 1.3 75.6 - - - +
262B TRP* 1.3 66.8 + - - +
264B GLY* 2.7 13.7 + - - +
265B ASN* 3.1 34.5 + - - -
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Residues in contact with TRP 262 (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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211B THR* 3.3 23.6 - - - +
213B PHE* 3.5 22.2 - + - -
221B TYR* 2.8 38.2 + + - -
223B ILE* 3.2 40.8 - - + -
236B PHE* 4.5 14.1 - + + -
238B ALA* 4.3 10.3 - - + -
250B LEU* 3.9 7.9 - - + -
254B LEU* 3.3 34.5 - - + -
258B LEU* 2.7 34.9 + - + +
259B ILE* 3.4 33.0 - - + +
261B HIS* 1.3 74.7 - - - +
263B LYS* 1.3 60.5 + - - +
264B GLY 3.5 0.3 + - - -
265B ASN* 3.5 5.2 + - - -
266B MET* 3.5 5.9 + - + +
359B LEU* 4.4 3.4 - - + -
361B VAL* 4.2 14.8 - - + -
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Residues in contact with LYS 263 (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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209B ASN* 3.7 20.0 - - - +
225B GLU* 3.0 28.2 + - - +
236B PHE* 3.7 17.5 - - + -
259B ILE 3.4 9.4 + - - +
260B SER* 3.1 14.3 + - - +
262B TRP* 1.3 79.0 - - - +
264B GLY* 1.3 61.8 + - - +
265B ASN 3.3 0.2 - - - -
266B MET* 3.5 23.9 + - - +
363B ARG* 4.0 20.4 - - - +
365B ASN* 4.9 6.5 - - - +
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Residues in contact with GLY 264 (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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260B SER 2.9 9.7 + - - -
261B HIS* 2.7 17.3 + - - -
263B LYS* 1.3 74.1 - - - +
265B ASN* 1.3 64.5 + - - -
266B MET 3.3 3.0 + - - +
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Residues in contact with ASN 265 (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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211B THR* 3.2 24.6 + - - +
213B PHE* 3.5 18.7 - - + -
261B HIS* 3.1 39.1 + - - -
262B TRP 3.5 0.6 + - - -
264B GLY* 1.3 81.6 + - - +
266B MET* 1.3 65.3 + - - +
267B THR* 4.4 3.6 + - - -
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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