Contacts of the strand formed by residues 256 - 261 (chain A) in PDB entry 3DK6
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 VAL 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SX7 3.2 53.8 - - + +
247A LYS* 3.9 1.6 - - - +
248A LEU* 2.9 50.4 + - + +
253A PHE* 3.7 29.8 - - + +
254A GLY 3.0 7.3 + - - +
255A GLU* 1.3 78.3 - - - +
257A TYR* 1.3 70.3 + - - +
269A ALA* 4.9 0.2 - - + -
270A VAL 3.3 4.5 - - - +
271A LYS* 4.3 9.4 - - + -
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Residues in contact with TYR 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A MET* 3.6 43.3 - - + -
246A HIS 3.5 6.3 - - - +
247A LYS* 3.6 33.7 - - + -
248A LEU* 4.0 6.7 - - - +
255A GLU* 2.7 39.2 + - - -
256A VAL* 1.3 76.7 - - - +
258A GLU* 1.3 66.4 + - - +
269A ALA* 3.4 6.6 - - - +
270A VAL 2.8 40.3 + - - +
272A THR* 3.8 17.7 - - - -
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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
----------------------------------------------------------
244A MET* 3.7 3.6 - - - -
245A LYS* 2.7 47.9 + - + +
246A HIS* 2.6 47.3 + - - +
248A LEU* 3.8 11.7 - - + +
257A TYR* 1.3 73.1 - - - +
259A GLY* 1.3 55.5 + - - +
267A THR* 3.7 21.8 + - + +
268A VAL 3.5 4.0 - - - -
317A PHE* 3.7 35.5 - - + -
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Residues in contact with GLY 259 (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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242A ILE* 4.3 5.2 - - - -
243A THR 3.2 12.6 - - - -
244A MET* 4.1 2.7 - - - -
245A LYS* 4.0 2.7 - - - -
257A TYR 3.7 1.6 + - - -
258A GLU* 1.3 75.9 - - - +
260A VAL* 1.3 62.1 + - - +
267A THR* 3.3 8.7 - - - +
268A VAL* 2.8 43.9 + - - -
270A VAL* 4.6 3.6 - - - +
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.3 9.0 - - - +
243A THR* 2.7 37.8 + - - +
245A LYS* 3.4 39.7 - - + +
259A GLY* 1.3 73.5 - - - +
261A TRP* 1.3 70.3 + - - +
262A LYS* 3.2 21.1 + - + +
265A SER* 4.3 14.8 - - - +
266A LEU 3.4 8.1 - - - +
267A THR* 5.1 4.3 - - - +
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Residues in contact with TRP 261 (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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237A MET* 3.5 33.7 - - + +
241A ASP* 3.8 21.0 - - + +
242A ILE* 3.8 14.4 - - + -
260A VAL* 1.3 68.5 - - - +
262A LYS* 1.3 66.5 + - - +
263A LYS* 4.3 10.2 - - + +
264A TYR* 3.0 42.6 + + + -
265A SER 3.0 18.2 + - - -
266A LEU* 2.8 32.7 + - + +
268A VAL* 4.1 21.2 - - + +
302A LEU* 3.8 42.8 - - + -
314A ILE* 5.2 0.9 - - + -
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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