Contacts of the strand formed by residues 255 - 261 (chain D) in PDB entry 2DFD
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 255 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239D ARG* 5.0 2.8 + - - -
253D GLY* 3.4 11.9 + - - +
254D VAL* 1.3 79.8 - - - +
256D GLU* 1.3 76.9 + - - +
273D PRO* 3.9 18.2 - - + -
274D LEU 3.2 9.2 - - - +
275D LEU* 3.9 13.7 - - + -
285D LEU* 3.9 30.3 - - + -
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Residues in contact with GLU 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D THR* 4.5 7.3 + - - +
156D ILE* 5.5 1.9 - - - +
239D ARG* 2.9 47.3 + - - +
240D PHE* 3.7 33.2 - - + -
243D SER* 2.6 39.2 + - - -
254D VAL 4.3 0.2 - - - -
255D VAL* 1.3 80.8 - - - +
257D CYS* 1.3 65.2 + - - +
258D SER* 4.8 0.2 - - - -
273D PRO* 4.2 1.6 - - - -
274D LEU* 2.8 36.8 + - - +
276D LEU* 4.1 9.4 - - + +
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Residues in contact with CYS 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D THR* 3.5 8.8 + - - -
153D THR* 4.3 7.8 + - - -
156D ILE* 3.7 23.0 - - + +
177D PRO* 4.1 6.5 - - - -
178D VAL 3.4 41.5 - - - +
240D PHE* 4.1 4.0 - - - -
255D VAL* 6.2 0.2 - - - -
256D GLU* 1.3 81.8 + - - +
258D SER* 1.3 63.1 + - - +
271D SER* 4.0 3.6 - - - +
272D THR 3.4 9.2 - - - +
273D PRO* 3.8 28.5 - - - -
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Residues in contact with SER 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D PHE* 3.4 24.3 - - - +
150D GLY 2.8 23.0 + - - -
152D THR* 3.7 2.9 - - - -
240D PHE* 3.8 20.1 - - - -
256D GLU 3.7 1.0 + - - -
257D CYS* 1.3 77.3 - - - +
259D PHE* 1.3 61.1 + - - +
260D VAL* 3.3 10.2 + - - +
270D PHE 3.7 1.2 - - - +
271D SER* 3.2 22.8 + - - -
272D THR 3.5 8.3 + - - +
274D LEU* 3.9 17.1 - - - +
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Residues in contact with PHE 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D VAL* 3.8 26.5 - - + -
127D ASN* 3.8 29.6 - - - -
130D ILE* 3.8 24.9 - - + +
131D PRO* 4.1 0.7 - - + -
149D PHE* 3.8 0.3 - - - -
150D GLY* 2.8 40.3 + - - +
152D THR* 3.7 19.0 - - + +
180D GLY 3.5 21.3 - - - -
181D GLY* 4.1 6.1 - - - -
258D SER* 1.3 69.6 + - - +
260D VAL* 1.3 57.7 + - - +
269D TYR* 3.5 31.4 - - + -
270D PHE* 3.6 16.4 - - - -
271D SER* 3.7 9.1 + - - -
305D LEU* 4.1 11.7 - - + -
309D ILE* 4.6 2.7 - - + -
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Residues in contact with VAL 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ILE* 4.9 1.1 - - - -
145D PRO 5.0 0.7 - - - +
148D ILE 3.4 23.3 - - - +
149D PHE* 3.8 13.9 - - + -
258D SER* 3.7 12.6 - - - +
259D PHE* 1.3 80.2 - - - +
261D LYS* 1.3 76.2 + - - +
262D SER 3.2 0.2 + - - -
269D TYR* 3.3 9.7 - - - -
270D PHE 3.0 32.8 + - - +
274D LEU* 3.7 32.5 - - + -
281D ILE* 3.9 20.0 - - + -
284D ASN* 4.4 6.7 - - - +
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Residues in contact with LYS 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ILE* 5.2 0.8 - - - +
138D LYS* 6.5 0.2 - - - -
143D TYR* 3.3 31.6 - - + +
145D PRO* 3.7 26.8 + - + +
148D ILE 5.0 1.6 + - - -
260D VAL* 1.3 81.8 - - - +
262D SER* 1.3 68.0 + - - +
263D GLN* 2.9 35.3 + - - +
268D THR* 2.9 39.4 + - - +
269D TYR* 3.6 21.7 - - + +
281D ILE* 5.1 3.5 - - - +
284D ASN* 4.6 2.9 + - - -
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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