Contacts of the helix formed by residues 256 - 269 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A LEU 3.4 7.6 - - - +
255A TYR* 1.3 89.4 - - + +
257A HIS* 1.3 67.8 + - - +
258A GLU* 3.6 23.6 - - - +
259A LYS* 2.9 33.4 + - + -
260A TYR* 3.0 12.1 + - - +
392A ARG* 4.2 0.2 - - - -
519A EDO 3.9 21.3 - - - +
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Residues in contact with HIS 257 (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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255A TYR 3.8 0.6 + - - -
256A PRO* 1.3 73.1 - - - +
258A GLU* 1.3 78.9 + - + +
259A LYS 3.3 0.5 + - - -
260A TYR* 3.4 15.0 + - - +
318A GLY 3.4 18.2 + - - -
320A VAL* 3.6 28.3 - - + +
323A HIS* 5.5 4.8 - - - -
391A LYS 5.1 0.4 - - - +
392A ARG* 2.9 40.4 + - - +
393A GLY 3.0 20.3 + - - -
395A PRO* 3.8 23.7 - - + +
519A EDO 4.8 1.4 + - - -
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Residues in contact with GLU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PRO* 3.6 17.8 - - - +
257A HIS* 1.3 99.4 + - + +
259A LYS* 1.3 72.5 + - + +
260A TYR 3.6 0.4 - - - -
261A VAL 5.4 0.8 + - - -
262A ALA* 5.7 0.9 + - - +
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Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A TYR* 4.7 2.7 - - + -
256A PRO* 2.9 35.3 + - + +
258A GLU* 1.3 91.4 - - + +
260A TYR* 1.3 65.3 + - - +
261A VAL 3.5 2.2 - - - -
262A ALA* 3.5 13.9 + - + +
263A ALA* 3.1 22.7 + - - +
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Residues in contact with TYR 260 (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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255A TYR* 4.2 13.5 - + + -
256A PRO 3.0 8.2 + - - +
257A HIS* 3.4 16.6 + - - +
258A GLU 3.6 0.6 - - - -
259A LYS* 1.3 74.0 - - - +
261A VAL* 1.3 72.1 + - + +
263A ALA* 3.1 11.8 + - - +
264A TRP* 3.2 43.2 + + - -
320A VAL* 3.5 24.9 - - + -
321A ARG* 3.6 26.4 - - + +
324A LEU* 4.1 12.7 - - + +
340A LYS* 4.7 3.6 + - - -
359A ARG* 4.0 7.0 + - - -
392A ARG* 3.6 35.0 - - - -
416A GLU* 2.7 39.5 + - - -
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLU 5.4 0.6 + - - -
259A LYS 3.5 0.2 - - - -
260A TYR* 1.3 76.0 - - + +
262A ALA* 1.3 63.8 + - - +
264A TRP* 3.1 13.2 + - - +
265A SER 4.2 0.3 + - - -
320A VAL* 3.8 19.0 - - + +
323A HIS* 3.8 30.7 - - + +
324A LEU* 4.0 15.7 - - + -
342A ARG* 3.5 51.3 - - - +
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Residues in contact with ALA 262 (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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258A GLU 5.7 0.9 + - - +
259A LYS* 3.5 16.7 + - + +
260A TYR 3.3 0.6 - - - -
261A VAL* 1.3 79.1 - - - +
263A ALA* 1.3 60.1 + - - +
264A TRP 3.1 1.6 + - - -
265A SER* 3.3 23.5 + - - -
268A ALA* 3.6 9.9 - - - +
342A ARG* 5.9 0.2 - - - +
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Residues in contact with ALA 263 (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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255A TYR* 3.5 45.5 + - + -
259A LYS 3.1 13.0 + - - +
260A TYR 3.1 14.8 + - - +
262A ALA* 1.3 76.4 - - - +
264A TRP* 1.3 52.3 + - + +
265A SER 3.3 2.4 + - - +
268A ALA* 4.0 18.1 - - - +
271A GLY* 5.8 0.2 - - - -
509A EDO 2.8 28.7 + - - -
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Residues in contact with TRP 264 (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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255A TYR* 5.4 1.2 - + - -
260A TYR* 3.2 48.8 + + - -
261A VAL 3.1 11.0 + - - +
263A ALA* 1.3 79.4 - - - +
265A SER* 1.3 58.8 + - - +
266A VAL 4.0 0.2 + - - -
324A LEU* 4.1 15.5 - - + +
340A LYS* 3.1 51.8 - - + +
341A LEU* 4.3 2.1 - - + -
342A ARG* 3.2 30.7 + - - -
353A CYS* 5.8 0.2 - - - -
356A VAL* 3.9 4.0 - - + -
359A ARG* 3.7 32.1 - - - -
420A GLU* 3.6 20.4 - - - -
505A EDO 3.9 20.9 - - - -
509A EDO 3.5 40.1 - - - -
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Residues in contact with SER 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A VAL 4.2 0.6 + - - -
262A ALA* 3.3 21.0 + - - -
263A ALA 3.3 1.1 - - - +
264A TRP* 1.3 80.4 - - - +
266A VAL* 1.3 59.6 + - - +
267A GLU* 2.9 31.5 + - - +
268A ALA* 2.8 29.5 + - - +
269A LYS* 3.9 2.1 + - - +
342A ARG* 3.5 16.1 + - - +
343A GLY 4.6 4.7 + - - -
344A THR* 5.7 0.2 - - - -
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Residues in contact with VAL 266 (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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264A TRP 4.0 0.2 + - - -
265A SER* 1.3 72.2 + - - +
267A GLU* 1.3 62.1 + - + +
268A ALA 3.2 1.3 - - - -
269A LYS* 3.5 27.5 - - - +
342A ARG 2.9 25.0 + - - +
343A GLY* 4.0 8.5 - - - -
344A THR* 3.9 26.2 - - + +
352A GLU* 3.8 39.9 - - + +
353A CYS* 3.6 30.3 - - - -
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Residues in contact with GLU 267 (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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265A SER* 2.9 17.4 + - - +
266A VAL* 1.3 79.3 - - + +
268A ALA* 1.3 57.3 + - - +
269A LYS 3.7 1.3 - - - -
344A THR* 3.8 32.2 - - + +
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Residues in contact with ALA 268 (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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262A ALA 3.6 24.0 - - - +
263A ALA* 4.0 17.1 - - - +
265A SER* 2.8 11.3 + - - +
267A GLU* 1.3 80.9 - - - +
269A LYS* 1.3 65.3 + - - +
270A PHE 3.7 0.2 + - - -
271A GLY* 3.6 14.5 + - - -
509A EDO 4.9 2.1 + - - -
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Residues in contact with LYS 269 (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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265A SER 4.6 1.6 - - - +
266A VAL* 3.5 34.3 + - - +
267A GLU 3.7 1.6 - - - -
268A ALA* 1.3 76.7 - - - +
270A PHE* 1.3 91.0 + - + +
271A GLY* 4.2 0.3 - - - -
277A GLU* 3.8 6.1 - - - +
280A ASN 2.7 24.4 + - - -
281A SER* 4.5 1.0 - - - +
352A GLU* 2.7 34.4 + - - +
353A CYS* 4.8 0.2 - - - +
354A ASN* 2.8 29.5 + - + +
509A EDO 6.1 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