Contacts of the helix formed by residues 256 - 265 (chain B) in PDB entry 3MYV
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 PRO 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254B LEU 3.4 7.6 - - - +
255B TYR* 1.3 88.3 - - + +
257B HIS* 1.3 66.9 + - - +
258B GLU* 4.4 4.9 - - + +
259B LYS* 2.9 36.8 + - + -
260B TYR* 3.1 11.3 + - - -
392B ARG* 4.2 0.4 - - - -
517B EDO 3.9 20.0 - - - +
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Residues in contact with HIS 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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332A GLY* 3.3 32.7 + - - -
255B TYR 3.8 0.8 + - - -
256B PRO* 1.3 72.8 - - - +
258B GLU* 1.3 69.3 + - + +
259B LYS 3.2 0.7 + - - -
260B TYR* 3.4 8.8 + - - +
261B VAL 5.0 0.2 + - - -
318B GLY 3.3 20.2 + - - -
320B VAL* 3.5 30.0 - - + +
391B LYS 5.1 0.2 - - - +
392B ARG* 2.8 40.3 + - - +
393B GLY 3.0 19.9 + - - -
395B PRO* 3.7 26.6 - - + +
517B EDO 4.8 1.6 + - - +
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Residues in contact with GLU 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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331A ALA* 3.5 48.6 - - + +
332A GLY* 4.5 2.7 - - - +
333A LYS* 3.7 27.6 - - - +
503A EDO 5.1 1.6 + - - -
256B PRO* 3.3 4.3 - - + +
257B HIS* 1.3 90.9 - - + +
259B LYS* 1.3 77.2 + - + +
260B TYR 3.6 0.8 + - - -
261B VAL 5.5 0.2 + - - -
262B ALA* 5.7 0.7 - - - +
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Residues in contact with LYS 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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331A ALA* 6.3 0.2 - - - +
255B TYR* 4.6 2.9 - - + +
256B PRO* 2.9 33.2 + - + +
258B GLU* 1.3 95.6 + - + +
260B TYR* 1.3 64.3 + - - +
261B VAL 3.4 2.2 - - - -
262B ALA* 3.5 16.3 + - + +
263B ALA* 3.1 22.4 + - - +
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Residues in contact with TYR 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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255B TYR* 4.3 13.2 - + + -
256B PRO 3.1 6.8 + - - +
257B HIS* 3.4 15.9 + - - +
258B GLU 3.6 0.6 - - - -
259B LYS* 1.3 75.1 - - - +
261B VAL* 1.3 70.6 + - + +
263B ALA* 3.1 10.0 + - - +
264B TRP* 3.1 44.9 + + - -
320B VAL* 3.7 28.3 - - + -
321B ARG* 3.5 25.9 - - + +
324B LEU* 4.2 12.7 - - + +
340B LYS* 4.6 2.8 + - - -
359B ARG* 4.0 5.9 + - - -
392B ARG* 3.5 35.2 - - - -
416B GLU* 2.7 41.0 + - - -
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Residues in contact with VAL 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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331A ALA* 6.0 2.7 - - - +
332A GLY 6.3 0.7 - - - +
503A EDO 3.5 25.5 + - - +
257B HIS 5.0 0.4 + - - -
258B GLU 5.5 0.6 + - - -
259B LYS 3.4 0.2 - - - -
260B TYR* 1.3 78.6 - - + +
262B ALA* 1.3 63.8 + - - +
264B TRP* 3.0 21.7 + - - +
320B VAL* 4.1 13.2 - - + +
323B HIS* 3.8 33.7 - - + +
324B LEU* 4.0 21.3 - - + -
342B ARG* 3.6 38.5 - - - +
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Residues in contact with ALA 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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78A GLU* 4.8 3.6 - - - +
503A EDO 3.5 26.4 + - - +
258B GLU 5.7 0.4 - - - +
259B LYS* 3.5 22.2 + - + +
260B TYR 3.3 0.2 - - - -
261B VAL* 1.3 78.6 - - - +
263B ALA* 1.3 61.3 + - - +
264B TRP 3.1 1.5 + - - -
265B SER* 3.2 22.9 + - - +
268B ALA* 3.7 7.8 - - - +
342B ARG* 5.8 0.7 - - - +
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Residues in contact with ALA 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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255B TYR* 3.6 46.7 - - + -
259B LYS 3.1 9.3 + - - +
260B TYR 3.1 15.2 + - - +
261B VAL 3.1 0.6 + - - -
262B ALA* 1.3 76.0 - - - +
264B TRP* 1.3 60.8 + - + +
265B SER 3.3 2.6 + - - +
268B ALA* 4.1 18.7 - - - +
508B EDO 2.9 21.0 + - - -
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Residues in contact with TRP 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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255B TYR* 5.3 1.3 - + - -
260B TYR* 3.1 49.2 + - - -
261B VAL* 3.0 11.6 + - - +
263B ALA* 1.3 80.2 - - - +
265B SER* 1.3 59.3 + - - +
266B VAL 3.9 0.2 + - - -
324B LEU* 4.1 14.9 - - + +
340B LYS* 3.3 61.3 - - + +
341B LEU* 4.2 1.3 - - + -
342B ARG* 3.1 32.8 + - - -
353B CYS* 5.3 0.5 - - - -
356B VAL* 3.7 15.0 - - + -
359B ARG* 3.7 27.8 - - - -
420B GLU* 3.7 12.8 - - - -
504B EDO 3.9 11.9 - - - -
508B EDO 3.5 39.2 - - - -
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Residues in contact with SER 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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261B VAL 4.2 0.8 + - - -
262B ALA* 3.2 20.3 + - - -
263B ALA 3.3 1.1 - - - +
264B TRP* 1.3 80.0 - - - +
266B VAL* 1.3 58.9 + - - +
267B GLU* 2.8 31.2 + - - +
268B ALA* 2.9 29.0 + - - +
269B LYS* 4.1 1.6 + - - +
342B ARG* 3.4 15.3 + - - +
343B GLY 5.1 3.0 + - - -
344B THR* 5.8 0.3 - - - -
353B CYS* 5.7 0.2 - - - -
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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