Contacts of the strand formed by residues 123 - 127 (chain D) in PDB entry 5EWL
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 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D ILE* 4.5 7.0 - - + -
97D VAL* 3.3 23.3 - - + +
99D PHE* 4.4 7.4 - - + -
112D LEU* 3.6 44.6 - - + +
115D ILE* 4.0 17.7 - - + -
116D SER* 3.7 19.3 - - - +
121D THR* 3.4 8.9 + - - +
122D PRO* 1.3 79.1 - - - +
124D LEU* 1.3 69.5 + - - +
142D MET 3.1 7.4 + - - +
143D PHE* 3.3 26.3 - - + -
144D PHE 3.0 24.6 + - - -
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Residues in contact with LEU 124 (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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97D VAL 2.8 15.7 + - - +
98D VAL* 3.7 19.7 - - + -
99D PHE* 2.7 33.4 + - - +
122D PRO* 5.5 5.6 - - + -
123D ILE* 1.3 78.6 - - - +
125D GLY* 1.3 58.5 + - - +
126D ILE* 3.3 16.6 + - + +
144D PHE* 3.1 39.7 - - + +
146D PHE* 4.7 17.3 - - + -
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Residues in contact with GLY 125 (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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99D PHE* 3.6 6.5 - - - -
124D LEU* 1.3 68.0 - - - +
126D ILE* 1.3 60.7 + - - -
127D HIS 3.5 2.5 - - - -
130D SER* 3.7 27.8 - - - -
131D SER* 3.4 8.3 - - - -
143D PHE* 3.7 9.7 - - - -
144D PHE 2.9 11.6 + - - -
145D GLN* 3.2 2.8 - - - -
146D PHE* 2.8 27.3 + - - -
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Residues in contact with ILE 126 (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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39D VAL* 6.0 0.9 - - + -
41D LEU* 5.6 3.4 - - + -
98D VAL* 3.9 25.4 - - + -
99D PHE 2.9 22.3 + - - +
100D ALA* 3.6 19.7 - - + -
124D LEU* 3.8 16.6 - - + +
125D GLY* 1.3 73.5 - - - -
127D HIS* 1.4 66.1 + - + +
131D SER* 4.1 2.0 - - - -
146D PHE* 3.5 58.5 - - + +
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Residues in contact with HIS 127 (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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100D ALA* 4.2 13.5 - - + -
101D ASP 3.0 41.0 + - - -
102D ASP* 4.9 5.2 - - - -
125D GLY 3.5 2.2 - - - -
126D ILE* 1.4 87.7 + - + +
128D GLY* 1.3 68.4 + - - +
130D SER* 2.7 22.6 + - - -
131D SER* 3.6 6.6 - - - -
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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