Contacts of the strand formed by residues 132 - 139 (chain P) in PDB entry 5A0Q
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 SER 132 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P VAL* 3.6 34.1 - - - +
75P TYR* 3.5 1.2 - - - +
76P SER* 2.9 33.3 + - - +
117P MET* 5.2 0.2 - - - -
130P GLY 3.6 1.0 + - - -
131P VAL* 1.3 72.6 - - - +
133P LEU* 1.3 61.4 + - - +
147P GLN* 3.1 5.9 + - - -
148P SER 2.9 8.1 + - - -
149P ASP* 2.1 35.9 + - - +
150P PRO* 4.0 3.8 - - - -
162P MET* 3.6 4.7 - - - +
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Residues in contact with LEU 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73P LEU* 2.8 25.6 - - + -
74P VAL 3.1 16.8 - - - +
75P TYR* 3.9 7.6 - - + -
82P TYR* 4.4 4.9 - - + -
85P LEU* 3.2 37.5 - - + -
113P VAL* 5.5 0.9 - - + -
117P MET* 5.9 2.5 - - - -
131P VAL* 3.9 13.7 - - + -
132P SER* 1.3 75.8 + - - +
134P LEU* 1.3 58.4 + - - +
135P ILE* 2.7 47.5 - - + +
147P GLN* 3.5 5.2 - - - -
148P SER* 2.9 38.0 + - - -
162P MET* 3.6 1.6 - - - -
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Residues in contact with LEU 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P SER* 4.6 1.8 - - - -
35P VAL* 3.6 39.7 - - - +
36P GLY* 3.7 6.5 - - - +
45P LEU* 3.9 24.1 - - + +
73P LEU* 3.3 5.0 - - - -
74P VAL* 2.9 33.2 + - + +
133P LEU* 1.3 72.5 - - - +
135P ILE* 1.3 59.6 + - - +
136P CYS 3.9 0.9 - - - -
145P LEU* 4.7 1.6 - - + -
146P PHE 3.2 9.0 - - - +
147P GLN* 3.5 10.8 - - - +
160P THR* 3.4 28.5 - - + +
162P MET* 2.9 39.5 - - + +
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Residues in contact with ILE 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67P ILE* 5.8 0.2 - - + -
71P ILE* 3.5 20.2 - - + -
72P GLY 3.4 15.7 - - - +
73P LEU* 3.5 9.2 - - + -
106P THR* 4.7 0.6 - - + +
109P LEU* 5.6 5.4 - - + -
110P VAL* 3.8 42.8 - - + +
113P VAL* 4.7 13.7 - - + -
133P LEU* 2.7 40.6 - - + +
134P LEU* 1.3 71.0 - - - +
136P CYS* 1.3 59.0 + - - +
137P GLY 3.9 0.3 + - - -
146P PHE* 2.9 35.8 + - + +
148P SER* 4.3 12.6 - - - +
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Residues in contact with CYS 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P VAL* 3.4 32.5 - - + -
45P LEU* 3.5 37.1 - - + +
71P ILE* 3.7 3.3 - - - -
72P GLY 3.3 25.8 + - - -
106P THR* 4.4 1.3 - - - -
134P LEU 3.9 1.4 - - - -
135P ILE* 1.3 71.3 - - - +
137P GLY* 1.3 56.8 + - - +
144P TYR 3.2 6.1 - - - +
145P LEU* 4.1 5.4 - - + +
210P GLY 5.6 0.7 - - - -
212P CYS* 3.8 11.0 - - - -
217P PHE* 3.7 21.8 - - - -
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Residues in contact with GLY 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P VAL* 5.3 1.5 - - - +
70P HIS 3.8 8.5 - - - -
71P ILE* 4.4 2.2 - - - -
106P THR* 3.3 22.2 - - - +
136P CYS* 1.3 69.8 - - - +
138P TRP* 1.3 54.6 + - - -
143P PRO* 3.4 0.4 - - - +
144P TYR* 2.0 68.2 + - - +
212P CYS* 4.4 2.9 - - - -
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Residues in contact with TRP 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P ALA 5.5 1.2 + - - -
41P ASN 4.2 7.7 + - - -
42P GLY* 4.4 7.4 - - - -
43P VAL 5.1 0.2 - - - -
70P HIS* 3.4 30.7 + - + +
71P ILE* 5.5 0.2 - - - +
106P THR* 3.9 1.6 + - - -
137P GLY* 1.3 72.7 - - - -
139P ASN* 1.3 70.8 + - - +
140P GLU* 3.2 28.5 - - - -
141P GLY* 3.3 33.0 - - - -
142P ARG 3.4 5.4 - - - -
143P PRO* 2.3 47.0 - - + +
212P CYS* 4.7 6.5 - - + -
213P ASN 3.5 26.9 + - - +
214P GLU* 5.1 20.9 - - + -
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Residues in contact with ASN 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70P HIS* 5.8 3.2 - - - +
71P ILE* 6.3 0.8 - - - +
103P PRO* 4.3 21.4 + - - +
104P ILE 4.5 3.2 + - - -
105P PRO* 3.5 8.4 - - + +
106P THR* 2.7 39.9 + - - -
138P TRP* 1.3 83.3 + - - +
140P GLU* 1.3 68.9 + - + +
141P GLY 3.0 0.5 + - - -
142P ARG 2.9 31.9 + - - +
144P TYR* 3.3 12.3 - - + +
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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