Contacts of the strand formed by residues 167 - 174 (chain D) in PDB entry 5D0A
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 VAL 167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74D ALA* 4.1 14.4 - - + -
75D LEU 3.1 8.7 - - - +
76D ALA* 3.8 11.2 - - + +
77D TYR* 3.5 9.6 - - - -
157D MET* 5.5 0.2 - - - +
158D ILE* 4.5 3.4 - - + +
160D THR* 4.4 19.7 - - + +
163D TYR* 3.7 30.7 - - + -
164D GLY 4.4 1.1 - - - +
165D SER 2.9 11.6 + - - +
166D TYR* 1.3 80.5 - - - +
168D TYR* 1.3 60.1 + - - +
169D LEU* 3.8 17.0 - - + -
503D B12 3.4 35.5 + - - +
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Residues in contact with TYR 168 (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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74D ALA* 3.2 7.6 - - - +
75D LEU 2.8 32.0 + - - +
77D TYR* 3.5 40.7 - + + +
98D ARG 3.5 7.1 + - - -
99D ALA* 3.3 36.0 + - + -
101D TRP 4.0 11.8 + - - -
103D LYS 5.4 2.4 + - - -
105D TYR* 3.4 51.4 + + + -
109D LEU* 3.7 21.7 - - + +
167D VAL* 1.3 73.1 - - - +
169D LEU* 1.3 59.8 + - - +
261D MET* 3.7 31.0 - - + -
503D B12 3.8 9.4 - - + -
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Residues in contact with LEU 169 (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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73D ILE 3.5 3.6 - - - +
74D ALA* 3.8 24.2 - - + -
109D LEU* 3.7 2.4 - - - +
133D VAL* 3.6 9.2 - - - +
140D ASP* 3.8 30.1 - - + +
141D ARG* 4.0 0.7 - - - -
144D ALA* 3.9 20.0 - - + -
149D ILE* 4.3 6.1 - - + -
158D ILE* 3.9 12.8 - - + -
167D VAL* 3.8 15.5 - - + -
168D TYR* 1.3 74.0 - - - +
170D ALA* 1.3 65.4 + - - +
503D B12 2.7 75.1 + - + +
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Residues in contact with ALA 170 (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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72D ALA* 3.6 2.8 - - - +
73D ILE* 2.8 40.4 + - + +
109D LEU* 3.6 19.7 - - + -
113D LEU* 4.0 9.9 - - + -
132D MET 3.6 13.5 - - - +
133D VAL* 3.7 12.3 - - + +
140D ASP* 5.1 0.4 - - - -
169D LEU* 1.3 77.2 - - - +
171D GLU* 1.3 76.0 + - - +
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Residues in contact with GLU 171 (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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70D ILE* 3.8 14.6 - - + -
71D VAL 3.1 13.5 - - - +
72D ALA* 3.9 1.1 - - - +
73D ILE 4.5 0.2 - - - +
113D LEU* 3.9 8.9 - - - +
130D LYS 4.2 0.5 - - - +
131D SER* 3.6 1.7 - - - -
132D MET* 3.0 49.1 + - + +
138D LEU* 3.8 19.9 - - + +
140D ASP* 2.7 49.6 - - - +
143D VAL* 3.9 22.5 - - + +
169D LEU* 5.1 0.3 - - - +
170D ALA* 1.3 89.5 + - - +
172D MET* 1.3 62.9 + - - +
173D ILE 5.4 0.4 - - - +
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Residues in contact with MET 172 (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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10D LEU* 5.1 2.2 - - + -
70D ILE* 3.6 2.0 - - - -
71D VAL* 2.7 61.2 + - + +
113D LEU* 4.1 11.7 - - + +
116D LEU* 4.2 17.5 - - + -
117D GLU* 4.1 20.4 - - - -
120D LEU* 3.7 22.0 - - + -
129D THR* 4.0 24.5 - - - -
130D LYS 3.5 4.7 - - - +
131D SER* 3.4 22.0 - - - +
171D GLU* 1.3 75.2 - - - +
173D ILE* 1.3 71.3 + - - +
174D THR* 3.6 7.9 + - + +
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Residues in contact with ILE 173 (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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60D PRO* 4.1 12.6 - - + +
63D LEU* 3.9 30.7 - - + -
64D LEU* 3.6 12.5 - - + +
67D ALA* 3.5 28.9 - - + -
69D SER 3.6 10.8 - - - +
70D ILE* 4.3 13.2 - - + +
129D THR* 3.2 6.2 - - - -
130D LYS* 2.9 39.6 + - + +
132D MET* 4.3 8.1 - - + -
138D LEU* 3.8 31.0 - - + -
171D GLU* 5.6 1.1 - - + -
172D MET* 1.3 72.8 - - - +
174D THR* 1.3 62.5 + - - +
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Residues in contact with THR 174 (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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64D LEU* 3.8 6.7 - - - -
67D ALA* 3.5 1.7 - - - -
68D LYS 2.8 21.3 + - - -
69D SER* 2.7 37.6 + - - +
71D VAL* 4.4 6.5 - - + -
120D LEU* 4.4 1.8 - - + -
128D ARG 3.3 9.4 - - - -
129D THR* 4.0 15.3 - - + -
172D MET* 3.7 25.8 - - + +
173D ILE* 1.3 79.7 - - - +
175D ASN* 1.3 60.7 + - - +
176D ILE* 3.0 30.5 + - + +
178D PHE* 4.2 0.6 - - + -
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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