Contacts of the strand formed by residues 57 - 62 (chain B) in PDB entry 5E97
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 LEU 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A TRP* 3.8 19.5 - - + -
369A LEU* 3.9 28.0 - - + -
380A VAL 3.9 2.0 - - - -
393A LEU* 5.7 0.4 - - + -
407A SER* 3.7 45.8 - - - +
410A PHE* 4.0 18.2 - - + -
411A LYS* 2.8 41.5 + - - +
55B SER 3.2 1.7 - - - +
56B PHE* 1.3 76.5 - - + +
58B SER* 1.3 71.7 - - - +
59B VAL* 4.6 9.8 - - + +
87B LEU* 4.4 5.9 - - + +
90B ALA* 3.6 7.1 - - - +
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A TRP* 4.8 0.2 - - - -
379A VAL* 4.0 2.5 - - - -
380A VAL 2.8 17.2 + - - +
381A MET* 3.8 12.8 - - - -
382A ARG* 2.9 22.3 + - - +
55B SER 2.7 22.0 + - - -
56B PHE 3.4 0.2 + - - -
57B LEU* 1.3 74.1 - - - +
59B VAL* 1.3 71.3 + - - +
90B ALA* 3.7 3.7 - - - -
91B TYR* 2.9 42.0 + - - +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 4.7 11.0 - - + -
381A MET* 4.7 1.7 - - - +
382A ARG* 3.5 11.7 - - + +
385A PHE* 4.0 21.5 - - + -
393A LEU* 3.9 27.1 - - + -
57B LEU* 4.6 4.9 - - + -
58B SER* 1.3 84.3 - - - +
60B THR* 1.3 64.8 + - - +
87B LEU* 4.0 19.7 - - + -
90B ALA* 5.4 4.0 - - + -
91B TYR 3.2 13.4 + - - +
92B LEU* 3.4 20.4 - - + -
93B ARG* 3.0 22.5 + - - +
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A GLY 4.2 3.6 - - - +
343A GLU* 4.5 4.7 - - + -
381A MET* 4.0 19.1 - - + +
382A ARG 2.9 24.7 + - - +
383A GLN* 2.8 27.3 + - - +
384A VAL* 3.3 9.9 - - - +
385A PHE* 2.8 32.9 + - - +
59B VAL* 1.3 77.6 - - - +
61B ILE* 1.3 65.6 + - - +
92B LEU* 4.0 2.7 - - - -
93B ARG* 3.2 29.6 - - - +
95B GLY 5.4 0.4 - - - -
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU* 4.8 5.2 - - + -
176A PHE* 4.8 4.7 - - + -
384A VAL* 3.8 2.0 - - - -
385A PHE* 4.3 9.0 - - + -
386A PHE* 3.5 33.9 - - + +
60B THR* 1.3 79.2 - - - +
62B ASP* 1.3 73.6 + - - +
65B LEU* 3.8 22.7 - - + -
71B PHE* 4.8 4.7 - - + -
75B LEU* 4.3 19.5 - - + -
92B LEU* 3.6 28.0 - - + +
93B ARG 2.9 8.0 + - - +
94B PHE* 3.3 20.7 - - + -
95B GLY 3.2 20.0 + - - +
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Residues in contact with ASP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A GLN* 2.8 22.4 + - - +
384A VAL* 3.6 7.5 - - - +
386A PHE 5.0 0.8 + - - -
60B THR* 4.4 0.2 + - - -
61B ILE* 1.3 77.3 - - - +
63B ALA* 1.3 68.8 + - - +
64B ASN* 2.9 29.9 + - + +
65B LEU* 2.9 23.5 + - + +
94B PHE* 3.8 1.7 - - - -
95B GLY 3.1 13.0 - - - +
96B GLY* 4.1 3.5 - - - -
97B THR 4.6 1.2 + - - -
98B LYS* 4.8 1.7 + - - +
1C BDP 2.7 29.0 + - - -
2C NDG 3.5 36.9 + - + +
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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