Contacts of the strand formed by residues 32 - 36 (chain C) in PDB entry 5LEZ
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 ALA 32 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C SER 4.4 1.6 - - - +
31C THR* 1.3 75.6 - - - +
33C VAL* 1.3 64.5 + - - +
44C GLY 3.5 7.6 - - - +
45C VAL* 4.2 8.3 - - + -
72C ALA* 4.5 9.2 - - + -
73C PHE 4.0 18.6 - - - +
132C LEU* 3.6 9.6 - - + +
160C ALA* 3.3 4.7 - - - +
161C ILE* 2.9 49.9 + - + +
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C THR* 4.6 6.7 - - + -
32C ALA* 1.3 79.7 - - - +
34C GLY* 1.3 69.7 + - - +
42C VAL 4.6 0.2 - - - -
43C LEU* 3.2 7.4 - - - +
44C GLY 2.7 37.5 + - - +
132C LEU* 3.8 5.4 - - - -
159C ASN 3.5 11.2 - - - +
160C ALA* 4.3 2.0 - - + -
168C VAL* 3.8 22.9 - - + -
172C LEU* 4.1 17.9 - - + -
191C VAL* 4.3 13.8 - - + +
194C ALA* 4.4 12.8 - - + -
195C LEU* 3.7 27.8 - - + +
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Residues in contact with GLY 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 1.3 74.5 - - - +
35C VAL* 1.4 66.4 + - - +
42C VAL 3.3 9.2 - - - -
43C LEU* 3.9 11.0 - - - -
132C LEU* 3.7 5.3 - - - +
144C LEU* 3.8 14.6 - - - -
158C ALA* 3.3 2.8 - - - +
159C ASN 2.9 33.2 + - - +
191C VAL* 5.3 0.2 - - - -
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Residues in contact with VAL 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 4.7 4.3 - - + -
34C GLY* 1.4 76.3 - - - +
36C ARG* 1.3 61.1 + - - +
37C GLY 3.5 3.8 + - - -
41C VAL* 3.6 3.3 - - - +
42C VAL* 3.1 33.0 + - - +
134C VAL* 5.8 1.1 - - - +
144C LEU* 4.2 3.5 - - - +
157C LYS 3.9 2.7 - - - -
158C ALA* 3.8 13.2 - - + +
172C LEU* 4.7 2.9 - - + -
176C TYR* 4.0 18.6 - - + -
181C ILE* 4.3 1.8 - - + -
187C THR* 3.7 24.2 - - + +
190C LEU* 4.1 18.8 - - + -
191C VAL* 3.1 37.9 - - + +
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Residues in contact with ARG 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C VAL* 1.3 71.1 - - - +
37C GLY* 1.3 74.1 + - - +
41C VAL* 4.1 7.6 - - + -
142C PRO* 3.5 38.7 + - + +
143C ARG* 4.0 15.2 - - - +
144C LEU* 4.1 15.0 - - + +
155C ALA* 5.8 0.8 - - - +
156C TRP 4.2 6.4 + - - -
157C LYS* 2.9 34.7 + - - +
176C TYR* 2.9 33.3 + - - -
181C ILE* 4.2 0.3 - - - +
60D GLU* 2.7 43.5 + - - +
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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