Contacts of the strand formed by residues 32 - 37 (chain B) in PDB entry 5ELI
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 32 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 3.8 42.0 - - + +
25B GLN 4.0 17.9 - - - +
26B GLY* 4.9 3.1 - - - -
30B GLN 4.0 0.2 + - - -
31B SER* 1.3 75.6 - - - +
33B GLN* 1.3 78.3 + - - +
34B VAL* 4.9 1.6 - - + -
95B ILE 3.9 0.3 - - - +
96B THR* 3.5 2.6 - - - +
97B LEU* 2.8 47.5 + - + +
100B LEU* 4.2 28.0 - - + -
126B VAL* 4.4 13.0 - - + -
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY* 4.9 12.6 - - - -
24B PHE* 3.7 16.8 - - - -
32B LEU* 1.3 82.6 - - - +
34B VAL* 1.3 61.4 + - - +
94B THR* 4.0 19.5 - - + +
95B ILE 3.4 3.8 - - - +
96B THR* 3.1 34.9 + - + +
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.4 48.9 - - + -
32B LEU* 4.9 6.5 - - + -
33B GLN* 1.3 74.1 - - - +
35B SER* 1.3 62.4 + - - +
36B CYS* 4.2 3.3 + - - -
50B TRP* 3.8 23.6 - - + -
93B LEU 3.9 0.3 - - - +
94B THR* 3.4 7.0 - - - +
95B ILE* 2.9 57.4 + - + +
97B LEU* 5.3 5.6 - - + -
122B ARG* 5.7 0.4 - - - +
124B VAL* 4.6 9.6 - - + -
126B VAL* 5.0 4.0 - - + -
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Residues in contact with SER 35 (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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78A TRP 4.4 0.2 + - - -
79A ASN* 3.1 30.9 + - - -
80A GLY 5.2 2.5 - - - -
201A NAG 4.1 6.5 - - - +
24B PHE* 4.5 5.5 - - - -
34B VAL* 1.3 74.8 - - - +
36B CYS* 1.3 61.2 + - - +
37B PRO* 3.4 10.7 - - - +
92B THR* 3.3 25.6 - - - +
93B LEU 3.3 4.9 - - - -
94B THR* 4.7 4.9 - - - +
122B ARG* 2.9 28.1 + - - -
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Residues in contact with CYS 36 (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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34B VAL* 4.2 2.9 - - - -
35B SER* 1.3 75.4 - - - +
37B PRO* 1.3 68.1 - - - +
38B TYR* 3.6 5.5 - - + -
50B TRP* 5.2 1.8 - - - -
93B LEU* 2.9 45.9 + - + -
95B ILE* 5.4 3.4 - - - -
110B CYS* 2.1 52.5 - - + -
121B LEU* 4.9 5.4 - - + -
122B ARG* 3.7 24.2 - - + +
124B VAL* 5.6 2.5 - - - -
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Residues in contact with PRO 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 4.0 20.6 - - - +
79A ASN* 6.5 0.2 - - - -
201A NAG 3.7 26.2 - - + -
35B SER* 3.4 16.2 - - - +
36B CYS* 1.3 85.5 - - - +
38B TYR* 1.3 66.1 + - - +
91B GLY 3.6 6.3 - - - +
92B THR* 4.6 4.9 - - + -
121B LEU* 4.7 11.8 - - - +
122B ARG* 4.8 6.9 - - + +
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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