Contacts of the strand formed by residues 66 - 73 (chain D) in PDB entry 3HU1
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 GLU 66 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D LEU* 3.8 23.5 - - + +
59D LEU 3.3 13.5 - - - +
60D LYS* 3.9 26.5 - - + +
64D ARG* 3.9 14.0 + - - +
65D ARG* 1.3 82.6 + - - +
67D ALA* 1.3 63.1 + - - +
91D ASN 3.9 8.8 - - - +
92D LEU* 3.8 4.5 - - - -
147D ARG* 2.9 47.3 + - - +
150D ASP* 3.9 9.7 - - - +
173D TYR* 4.5 6.4 - - - -
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Residues in contact with ALA 67 (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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57D VAL 3.8 0.5 - - - +
58D LEU* 3.8 4.1 - - - +
59D LEU* 2.9 38.0 + - + +
66D GLU* 1.3 76.6 - - - +
68D VAL* 1.3 65.6 + - - +
69D CYS* 4.9 1.6 - - - -
88D VAL* 4.4 17.5 - - + -
91D ASN* 4.6 11.0 - - + +
92D LEU* 3.9 18.4 - - + -
147D ARG* 4.8 2.7 - - - -
150D ASP* 4.6 8.5 - - - +
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Residues in contact with VAL 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ASN 5.5 0.2 - - - +
37D SER* 4.8 2.4 - - - +
56D THR* 6.0 1.3 - - - -
57D VAL 3.3 11.9 - - - +
58D LEU* 4.2 13.0 - - + -
67D ALA* 1.3 75.6 - - - +
69D CYS* 1.3 63.8 - - - +
105D CYS* 4.4 14.6 - - - -
108D VAL* 5.5 4.7 - - + -
145D PRO* 3.3 31.1 - - + +
146D ILE 3.5 41.7 - - - +
147D ARG* 3.7 4.6 - - + +
150D ASP* 5.0 3.0 + - - +
173D TYR* 4.1 26.9 - - + -
174D CYS 5.1 0.7 - - - +
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Residues in contact with CYS 69 (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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36D ASN 4.4 2.2 - - - -
37D SER 3.4 19.1 - - - +
39D VAL* 3.6 40.4 - - + -
56D THR* 3.3 6.4 - - - -
57D VAL* 2.8 37.4 + - + -
59D LEU* 3.8 13.7 - - + -
67D ALA* 4.0 3.8 - - - -
68D VAL* 1.3 79.1 - - - +
70D ILE* 1.3 60.3 + - - +
88D VAL* 4.0 19.1 - - - -
145D PRO* 3.9 7.1 - - - +
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Residues in contact with ILE 70 (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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35D ASP* 5.9 0.4 - - - +
37D SER* 2.7 27.4 + - - +
38D VAL* 3.5 11.4 - - + +
39D VAL* 3.1 24.0 + - - +
54D GLY* 3.3 36.6 - - - +
55D ASP 3.4 4.7 - - - +
56D THR* 4.3 15.7 - - + +
69D CYS* 1.3 73.6 - - - +
71D VAL* 1.3 60.2 + - - +
72D LEU* 5.2 7.2 - - + -
142D ALA 5.7 1.6 - - - +
143D TYR* 4.6 16.6 - - + +
145D PRO* 4.2 6.0 - - + +
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Residues in contact with VAL 71 (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 VAL* 3.5 15.3 - - + +
41D LEU* 3.8 32.5 - - + -
46D MET* 4.0 13.7 - - + -
51D LEU* 4.3 8.5 - - + -
52D PHE 3.8 18.2 - - - +
53D ARG* 3.7 1.6 - - - -
54D GLY* 2.6 34.0 + - - -
55D ASP* 3.0 24.9 + - + +
57D VAL* 3.8 26.0 - - + +
69D CYS 4.2 0.2 - - - -
70D ILE* 1.3 72.5 - - - +
72D LEU* 1.3 62.5 - - - +
102D ILE* 4.7 2.0 - - + -
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Residues in contact with LEU 72 (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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33D ASN* 4.1 15.5 - - - +
38D VAL* 3.6 28.7 - - + -
39D VAL 3.1 7.2 + - - +
40D SER* 3.4 9.1 - - - +
41D LEU 3.1 24.4 + - - +
46D MET* 4.0 6.8 - - - +
53D ARG* 3.9 37.2 - - + +
54D GLY* 4.0 15.3 - - - +
70D ILE* 4.9 7.0 - - + +
71D VAL* 1.3 82.9 - - - +
73D SER* 1.3 61.8 + - - +
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Residues in contact with SER 73 (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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40D SER* 5.4 0.2 - - - -
41D LEU 3.4 7.0 - - - -
43D GLN* 3.2 36.5 + - - -
46D MET* 3.8 11.0 - - - -
53D ARG* 4.1 22.1 + - - +
72D LEU* 1.3 75.2 - - - +
74D ASP* 1.3 59.7 + - - +
75D ASP* 4.3 7.1 + - - +
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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