Contacts of the strand formed by residues 122 - 130 (chain D) in PDB entry 5DIR
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 122 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D ALA 3.6 1.4 - - - +
53D TYR* 3.6 1.0 - - - -
54D ASN* 2.9 39.1 + - - +
112D ASN* 3.4 30.3 - - + +
115D ASP* 3.9 7.0 - - - +
116D ARG* 3.6 51.6 - - + +
121D HIS* 1.3 76.0 - - - +
123D VAL* 1.3 65.5 + - - +
140D ASN* 3.6 8.5 - - - +
203G SER* 3.5 26.7 - - - -
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Residues in contact with VAL 123 (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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27D LYS* 3.8 30.3 - - + +
30D PHE* 5.8 0.7 - - + -
31D GLN* 3.5 33.4 - - + +
51D LEU* 3.8 26.7 - - + -
52D ALA 3.6 4.3 - - - +
53D TYR* 4.1 7.4 - - + -
115D ASP* 3.5 7.0 + - - +
119D LEU* 3.7 20.6 - - + -
121D HIS* 4.5 0.7 - - + -
122D VAL* 1.3 71.6 - - - +
124D ASP* 1.3 75.9 + - - +
125D PHE* 4.4 4.3 - - + -
140D ASN* 2.9 22.2 + - - +
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Residues in contact with ASP 124 (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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50D THR* 4.0 1.0 - - - +
51D LEU* 3.5 5.5 - - - +
52D ALA* 2.9 40.7 + - + +
54D ASN* 3.2 30.0 + - - +
122D VAL 4.2 3.1 - - - -
123D VAL* 1.3 85.0 - - - +
125D PHE* 1.3 61.8 + - - +
138D ALA* 2.9 41.4 - - + +
139D PHE* 3.7 5.2 - - - -
140D ASN* 3.5 5.2 + - - -
203G SER* 3.1 21.8 + - - -
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Residues in contact with PHE 125 (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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23D ASP 4.9 0.2 - - - -
26D SER* 3.4 22.2 - - - -
27D LYS* 4.1 20.9 - - + -
30D PHE* 3.5 44.6 - + + -
49D TRP* 3.3 18.4 - + - -
50D THR* 2.8 45.8 + - - +
51D LEU* 5.5 1.1 - - + -
123D VAL* 4.9 2.2 - - + -
124D ASP* 1.3 75.8 - - - +
126D ILE* 1.3 83.2 + - + +
127D LEU 3.9 0.2 - - - -
139D PHE 3.0 2.8 + - - -
140D ASN* 3.7 17.9 - - + -
141D LEU* 3.4 36.1 - - + -
202D OLC 5.1 2.0 - - + -
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Residues in contact with ILE 126 (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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47D PHE* 3.5 27.4 - - + -
48D SER 4.2 1.6 - - - -
49D TRP* 4.2 8.3 - - + -
124D ASP 4.0 0.2 - - - -
125D PHE* 1.3 101.5 - - + +
127D LEU* 1.3 58.5 + - - +
128D VAL* 4.4 3.6 - - + -
138D ALA* 3.3 5.5 - - - -
139D PHE* 2.9 77.3 + - + +
140D ASN 3.9 18.8 - - - +
141D LEU* 4.4 6.5 - - + +
144D SER* 4.4 3.1 - - - +
202D OLC 5.9 1.8 - - + -
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Residues in contact with LEU 127 (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 GLN* 3.3 34.8 - - + +
47D PHE* 3.6 4.0 - - - -
48D SER* 3.0 42.9 + - - +
50D THR* 3.9 19.1 - - + -
125D PHE 3.6 0.4 + - - -
126D ILE* 1.3 72.7 - - - +
128D VAL* 1.3 60.3 + - - +
129D HIS* 3.7 7.3 - - + -
135D TYR* 3.8 31.2 - - + -
136D PHE 3.4 23.6 - - - +
138D ALA* 4.2 14.4 - - + +
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Residues in contact with VAL 128 (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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46D LEU 3.3 8.1 - - - +
47D PHE* 4.4 10.8 - - + -
126D ILE* 3.9 4.2 + - + -
127D LEU* 1.3 74.5 - - - +
129D HIS* 1.3 67.3 + - - +
134D TRP* 4.7 7.4 - - + -
135D TYR* 3.8 0.3 - - - +
136D PHE* 2.8 39.9 + - + +
139D PHE* 4.0 26.5 - - + -
205D OLC 3.9 53.6 - - + -
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Residues in contact with HIS 129 (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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43D ILE 4.4 0.4 + - - -
44D PRO 3.5 17.0 + - - -
45D ASP 3.1 24.2 - - - +
46D LEU* 2.8 53.1 + - - +
47D PHE* 3.8 3.2 + - - -
48D SER* 4.0 14.3 + - - -
127D LEU* 3.7 16.8 - - + -
128D VAL* 1.3 75.5 - - - +
130D TRP* 1.3 60.0 + - - +
131D GLN* 2.8 32.6 + - - -
134D TRP* 3.1 24.2 - - - +
135D TYR* 3.4 31.9 - + + +
205D OLC 4.4 2.9 - - - +
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Residues in contact with TRP 130 (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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45D ASP* 3.4 30.1 - - + -
46D LEU* 3.6 21.5 - - + -
129D HIS* 1.3 72.0 - - - +
131D GLN* 1.3 100.7 + - - +
133D ARG* 2.9 39.3 + - + +
134D TRP* 2.7 13.4 + - - +
204D OLC 2.9 54.5 + - + -
205D OLC 3.7 33.4 - - + +
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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