Contacts of the strand formed by residues 83 - 87 (chain D) in PDB entry 3ELP
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 TYR 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D ALA* 3.9 4.7 - - - -
81D ALA* 3.5 2.9 - - - +
82D LYS* 1.3 127.3 + - + +
84D CYS* 1.3 62.6 + - - +
85D LEU* 6.0 0.2 - - + -
226D SER* 3.3 7.4 - - - -
227D VAL* 2.9 37.2 + - + +
228D ASN 3.9 9.4 - - - -
229D CYS 3.5 15.0 - - - -
230D GLU* 2.7 33.8 + - - -
233D HIS* 3.3 55.0 - + + +
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Residues in contact with CYS 84 (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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72D GLU* 3.5 44.8 - - - +
75D VAL* 3.6 24.9 - - - -
76D ALA* 3.8 5.6 - - - +
83D TYR* 1.3 78.8 - - - +
85D LEU* 1.3 88.1 + - - +
224D LEU* 4.1 10.5 - - - -
225D VAL 3.3 13.2 - - - -
226D SER* 3.3 19.5 - - - +
233D HIS* 4.8 3.7 - - - -
237D ARG* 4.3 0.7 + - - -
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Residues in contact with LEU 85 (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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72D GLU* 3.1 4.9 - - - -
84D CYS* 1.3 82.9 - - - +
86D ALA* 1.3 58.8 + - - +
87D PHE* 3.6 19.0 - - + -
223D GLY 3.4 3.5 - - - +
224D LEU* 3.6 0.9 - - - -
225D VAL* 2.7 44.1 + - + +
227D VAL* 5.2 4.0 - - + -
233D HIS* 4.0 19.5 - - + +
236D LEU* 3.0 48.7 - - + -
237D ARG* 3.4 42.4 - - - +
240D GLN* 3.5 11.2 - - - +
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Residues in contact with ALA 86 (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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68D ARG* 4.1 14.4 - - + -
71D LEU* 4.4 4.3 - - + -
72D GLU* 2.7 21.0 + - + +
85D LEU* 1.3 71.7 - - - +
87D PHE* 1.3 65.7 + - - +
222D MET* 4.1 6.3 - - - -
223D GLY 3.3 4.3 - - - -
224D LEU* 3.9 17.9 - - + -
240D GLN* 3.0 19.6 + - - +
246D VAL* 4.1 0.3 - - - +
247D PRO* 3.5 24.4 - - + +
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Residues in contact with PHE 87 (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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85D LEU* 3.6 29.6 - - + -
86D ALA* 1.3 75.6 - - - +
88D ALA* 1.3 60.5 + - - +
89D SER 3.1 12.8 - - - +
92D ALA 4.4 2.0 - - - -
93D ALA* 4.0 12.3 - - - +
96D THR* 3.6 41.1 - - + -
97D ILE* 6.1 0.2 - - + -
222D MET* 3.6 1.7 - - - +
223D GLY 2.6 41.6 + - - +
225D VAL* 3.7 23.1 - - + -
236D LEU* 4.4 6.3 - - + -
240D GLN* 3.8 35.4 - - + -
245D ALA* 3.2 20.6 - - + +
247D PRO* 3.3 14.4 - - - +
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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