Contacts of the strand formed by residues 271 - 276 (chain D) in PDB entry 6E7P
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 ILE 271 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 3.7 38.1 - - + -
118D ALA* 3.3 3.6 - - - -
119D ALA* 3.0 37.0 + - + +
125D LEU* 3.7 23.3 - - + -
225D PHE* 5.8 0.4 - - + -
228D LEU* 5.1 6.1 - - + -
262D PHE* 3.8 26.0 - - + +
263D ASP 3.3 15.7 - - - +
264D ASN* 4.0 24.0 - - + +
270D ARG* 1.3 76.0 - - - +
272D PRO* 1.3 72.6 - - - +
273D ILE* 4.2 2.4 - - + +
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Residues in contact with PRO 272 (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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96A GLU* 5.1 2.0 - - - +
115D ASP 5.8 3.6 - - - +
117D PHE 3.8 8.7 - - - +
118D ALA* 4.3 2.9 - - + -
261D THR 3.6 1.1 - - - +
262D PHE* 3.7 0.3 - - - -
263D ASP* 3.2 47.3 + - + +
264D ASN* 5.4 0.2 - - - -
270D ARG* 3.3 33.4 - - - +
271D ILE* 1.3 91.9 - - - +
273D ILE* 1.3 62.6 + - - +
274D SER* 5.0 5.2 - - - +
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Residues in contact with ILE 273 (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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106D LEU* 3.7 31.3 - - + +
114D ASP 4.5 10.0 - - - +
117D PHE* 3.3 46.9 + - + +
118D ALA 4.5 3.1 - - - -
119D ALA* 4.2 20.9 - - + -
128D ALA* 4.4 9.6 - - + -
260D ILE* 4.8 1.8 - - + -
261D THR 3.5 4.7 - - - +
262D PHE* 3.7 37.7 - - + -
271D ILE 4.2 5.4 - - - +
272D PRO* 1.3 80.7 - - - +
274D SER* 1.3 68.8 + - - +
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Residues in contact with SER 274 (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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106D LEU* 4.6 4.9 - - - +
259D LEU 4.4 0.4 - - - -
260D ILE* 3.6 11.1 - - - +
261D THR* 3.2 40.5 + - - +
263D ASP* 6.0 1.7 - - - +
272D PRO* 5.0 5.5 - - - +
273D ILE* 1.3 80.8 + - - +
275D LEU* 1.3 65.6 + - - +
276D GLU* 5.0 9.0 - - - -
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Residues in contact with LEU 275 (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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486C ARG* 4.2 2.8 + - - -
98D THR* 4.7 7.4 - - - +
101D PHE* 4.3 28.9 - - + +
102D ARG* 3.9 52.8 + - + +
105D PHE* 4.6 2.0 - - + -
106D LEU* 4.6 11.4 - - + -
258D VAL* 4.3 14.8 - - + -
259D LEU 3.4 6.1 - - - -
260D ILE* 4.1 21.3 - - + -
274D SER* 1.3 76.3 - - - +
276D GLU* 1.3 88.6 + - - +
277D THR* 4.4 11.4 - - + -
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Residues in contact with GLU 276 (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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486C ARG* 2.5 46.9 + - - +
257D SER 3.3 4.4 - - - +
258D VAL* 3.3 2.8 - - - -
259D LEU* 3.2 48.8 + - + +
261D THR* 5.5 2.7 - - - +
274D SER* 5.0 7.3 - - - -
275D LEU* 1.3 84.0 + - - +
277D THR* 1.3 70.5 + - - +
278D GLN* 4.4 14.1 + - - +
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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