Contacts of the strand formed by residues 130 - 137 (chain D) 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 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D GLN* 5.2 0.2 + - - -
26D VAL* 3.4 25.9 - - - +
74D ALA* 3.0 27.4 + - - +
128D GLY 4.1 0.6 + - - -
129D ILE* 1.3 71.2 - - - +
131D ALA* 1.3 62.2 + - - +
132D LEU* 3.8 0.7 + - - +
147D THR 3.1 15.9 - - - -
148D ASP* 3.7 5.9 - - - +
149D PRO* 3.3 21.8 - - - +
161D ILE* 3.6 25.6 - - - +
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Residues in contact with ALA 131 (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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71D MET* 3.8 31.6 - - + -
73D PHE* 3.9 10.1 - - + +
111D ILE* 5.2 1.1 - - + -
115D LYS* 3.5 14.6 - - - +
129D ILE* 4.0 2.4 - - + -
130D SER* 1.3 72.1 - - - +
132D LEU* 1.4 58.1 + - - +
133D ILE* 3.3 24.1 + - + -
146D GLN* 3.7 1.6 - - - -
147D THR* 3.0 30.1 + - - -
161D ILE* 4.7 0.9 - - - -
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Residues in contact with LEU 132 (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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32D ALA* 3.4 34.8 - - + +
33D VAL 4.1 2.7 - - - +
34D GLY* 3.9 15.9 - - - +
43D LEU* 5.9 0.4 - - + -
71D MET* 3.8 0.2 - - - -
72D ALA* 3.0 49.2 + - + +
74D ALA* 4.9 0.4 - - + -
130D SER 4.3 3.4 - - - +
131D ALA* 1.4 69.3 - - - +
133D ILE* 1.4 61.4 + - - +
134D VAL* 3.4 14.1 + - + +
144D LEU* 4.5 10.8 - - + -
145D TYR 3.5 11.4 - - - +
159D ASN* 3.6 26.2 - - + +
161D ILE* 3.7 27.8 - - + -
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Residues in contact with ILE 133 (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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65D LEU* 5.1 2.0 - - + -
69D VAL* 3.8 20.4 - - + -
70D CYS 3.7 11.7 - - - +
71D MET* 4.0 11.4 - - - +
104D VAL* 4.1 5.4 - - + -
107D ILE* 4.0 7.6 - - + -
108D THR* 3.8 31.4 - - - +
111D ILE* 3.5 32.3 - - + -
131D ALA* 3.3 18.1 + - + -
132D LEU* 1.4 69.1 - - - +
134D VAL* 1.3 63.1 + - - +
145D TYR* 3.1 34.7 + - + +
147D THR* 3.5 22.2 - - - +
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Residues in contact with VAL 134 (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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41D VAL* 3.5 39.9 - - + -
43D LEU* 3.8 21.5 - - + -
69D VAL* 3.6 0.7 - - - +
70D CYS* 2.8 42.2 + - - +
104D VAL* 3.5 11.4 - - - +
132D LEU* 3.4 16.8 - - + +
133D ILE* 1.3 77.9 - - - +
135D GLY* 1.3 62.6 + - - +
143D ARG 3.4 7.6 - - - +
144D LEU* 4.0 26.5 - - + -
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Residues in contact with GLY 135 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D VAL* 4.5 3.1 - - - +
68D ASN 3.2 15.3 - - - -
70D CYS* 4.4 2.7 - - - -
104D VAL* 3.4 16.4 - - - +
134D VAL* 1.3 84.7 - - - +
136D PHE* 1.3 68.2 + - - -
142D PRO 3.9 0.2 - - - -
143D ARG* 3.2 28.3 + - - +
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Residues in contact with PHE 136 (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 ASP 4.5 1.1 - - - -
40D ILE* 3.0 51.4 - - + -
41D VAL* 3.8 15.7 - - + -
68D ASN* 3.4 27.7 + - + +
104D VAL* 3.1 16.2 - - - +
135D GLY* 1.3 74.7 - - - -
137D ASP* 1.4 58.5 + - - +
140D GLY 3.3 26.5 - - - -
141D THR 3.8 5.4 - - - -
142D PRO* 4.9 4.9 - - + -
211D MET* 3.5 29.4 - - + -
212D ARG 3.4 19.5 - - - -
213D ARG* 3.4 36.8 - - - +
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Residues in contact with ASP 137 (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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68D ASN* 5.7 2.3 - - - +
103D THR* 3.6 10.4 + - - +
104D VAL* 3.8 3.5 - - - +
105D GLU* 2.8 33.1 - - - +
136D PHE* 1.4 75.1 - - - +
140D GLY* 3.0 29.1 + - - +
141D THR* 2.8 32.4 + - - +
143D ARG* 3.1 22.9 + - - +
213D ARG* 3.4 15.5 + - - -
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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