Contacts of the strand formed by residues 99 - 110 (chain D) in PDB entry 5J0Z
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 THR 99 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D SER* 4.4 9.0 - - - +
47D TRP 3.4 14.4 - - - +
48D LYS* 4.1 15.9 - - + +
93D SER 4.0 0.2 - - - +
94D VAL* 3.5 1.6 - - - -
95D SER* 2.7 50.3 + - - +
97D ASP* 2.6 26.9 + - - -
98D GLY* 1.3 77.6 - - - +
100D VAL* 1.3 68.6 + - - +
101D GLN* 5.8 2.0 - - + -
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Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D SER* 3.0 29.7 + - - -
47D TRP* 2.7 59.6 + - + +
49D ASP* 4.3 0.7 - - + -
52D LEU* 3.9 23.6 - - + -
71D ILE* 3.6 22.9 - - + -
92D ILE* 3.7 17.5 - - + -
93D SER 3.5 5.2 - - - +
94D VAL* 4.2 6.1 - - + +
98D GLY 4.1 6.1 - - - +
99D THR* 1.3 76.7 - - - +
101D GLN* 1.3 65.8 + - - +
102D TYR 4.1 0.4 - - - -
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Residues in contact with GLN 101 (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 LEU 3.8 1.4 + - - -
46D SER* 3.0 29.5 + - - +
91D ASP* 3.5 3.3 - - - +
92D ILE* 3.3 4.0 - - - -
93D SER* 2.7 49.6 + - - +
95D SER* 5.1 8.5 - - - +
99D THR* 5.5 2.0 - - + -
100D VAL* 1.3 76.7 - - - +
102D TYR* 1.3 58.9 + - - +
103D LEU* 5.5 0.2 - - - +
145D ASP* 5.4 1.0 + - - -
148D LYS* 3.7 27.7 + - - +
178E ASP* 5.1 6.2 - - - +
179E ARG* 6.1 0.4 - - - +
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Residues in contact with TYR 102 (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 LEU 4.5 1.1 - - - -
44D SER* 3.4 5.2 - - - -
45D LEU* 2.8 65.1 + - + +
47D TRP* 3.6 23.3 - + + -
68D PRO* 5.6 0.4 - - + -
73D ILE* 4.0 35.2 - - + -
85D ARG* 5.2 2.4 + - - -
89D VAL* 3.9 28.4 - - + +
91D ASP 3.6 2.2 - - - -
92D ILE* 3.9 18.6 - - + +
100D VAL* 4.1 1.2 - - + -
101D GLN* 1.3 73.3 - - - +
103D LEU* 1.3 64.3 + - - +
104D GLU* 3.0 47.8 + - + +
148D LYS* 5.4 1.9 + - - -
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Residues in contact with LEU 103 (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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42D PHE* 3.9 25.6 - - + -
43D LEU 3.7 6.7 - - - +
44D SER* 3.6 27.8 - - - -
89D VAL* 3.7 2.8 - - - +
90D VAL* 2.7 51.5 + - + +
91D ASP* 2.9 23.0 + - + +
101D GLN 5.5 0.2 - - - +
102D TYR* 1.3 79.8 - - - +
104D GLU* 1.3 57.3 + - - +
148D LYS* 5.5 1.8 - - - +
133E ARG* 3.6 36.6 - - - +
177E GLU* 3.6 14.6 - - - +
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Residues in contact with GLU 104 (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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42D PHE* 3.3 7.4 - - - +
43D LEU* 2.8 60.1 + - + +
85D ARG* 2.6 44.4 + - - -
87D ALA* 3.4 18.1 - - + +
88D ASP 3.2 18.2 - - - +
89D VAL* 4.3 0.6 - - - +
90D VAL* 3.7 3.8 - - - -
102D TYR* 3.0 30.7 + - + +
103D LEU* 1.3 75.3 - - - +
105D ARG* 1.3 61.4 + - - +
106D PHE* 4.0 2.2 - - - +
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Residues in contact with ARG 105 (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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25D ILE* 3.4 20.9 - - + +
40D ASN* 3.1 31.9 + - - +
41D ALA 3.5 10.5 - - - +
42D PHE* 3.6 25.6 - - + -
86D ASP 4.2 0.2 - - - +
87D ALA* 3.4 1.9 - - - -
88D ASP* 3.0 38.8 + - - +
90D VAL* 3.4 9.1 - - + +
104D GLU* 1.3 74.2 - - - +
106D PHE* 1.3 61.5 + - - +
77E ARG* 4.1 25.0 - - - +
78E PHE 2.8 23.0 + - - -
79E VAL 2.8 27.9 + - - -
81E VAL* 4.9 2.7 + - - +
403E ACT 3.0 20.7 + - - -
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Residues in contact with PHE 106 (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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22D ILE* 4.2 10.8 - - + -
39D VAL* 3.9 26.0 - - + -
40D ASN* 3.3 7.0 - - - +
41D ALA* 2.8 79.3 + - + -
42D PHE 4.1 1.8 - - - -
43D LEU* 3.9 24.2 - - + -
78D PHE* 3.3 44.6 - + - -
85D ARG* 3.7 24.2 - - + -
86D ASP 3.3 10.5 - - - +
87D ALA* 4.1 1.8 - - + -
104D GLU* 4.0 4.7 - - - +
105D ARG* 1.3 74.2 - - - +
107D SER* 1.3 67.4 - - - +
108D ALA* 4.1 4.7 - - + -
110D VAL* 6.1 0.2 - - + -
128D ILE* 5.3 2.7 - - + -
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Residues in contact with SER 107 (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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28D TYR* 4.5 8.1 - - - -
39D VAL 3.1 16.4 - - - -
40D ASN* 3.9 20.2 - - - -
83D ASN* 5.9 0.2 - - - +
86D ASP* 3.1 40.1 + - - +
106D PHE* 1.3 79.3 - - - +
108D ALA* 1.3 60.5 + - - +
82E GLU 4.0 10.7 + - - -
84E ALA* 5.5 5.2 - - - +
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Residues in contact with ALA 108 (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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38D LYS* 3.5 5.3 - - - +
39D VAL* 3.0 37.9 + - + +
78D PHE* 5.2 0.9 - - + -
81D VAL* 4.2 16.6 - - + -
83D ASN* 3.9 20.2 - - - +
85D ARG* 4.0 15.7 - - + -
106D PHE* 4.1 12.6 - - + -
107D SER* 1.3 75.2 - - - +
109D ARG* 1.3 62.0 + - - +
110D VAL* 3.7 1.0 + - + -
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Residues in contact with ARG 109 (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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401C SO4 3.2 33.9 + - - -
31D ASP* 4.3 5.7 + - - +
34D ALA* 3.7 14.1 - - - +
36D THR* 3.4 39.6 + - - +
37D PHE 3.8 5.4 - - - +
38D LYS* 3.8 37.3 - - + +
81D VAL* 3.3 6.0 - - - +
82D GLU* 3.2 49.8 + - - +
83D ASN* 3.7 29.5 + - + +
108D ALA* 1.3 72.7 - - - +
110D VAL* 1.3 60.6 + - - +
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Residues in contact with VAL 110 (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 THR* 3.2 8.4 - - - -
37D PHE* 2.9 62.3 + - + +
39D VAL* 4.0 28.0 - - + -
80D ASN* 3.4 17.5 - - - +
81D VAL* 4.1 12.1 - - + -
82D GLU* 5.6 0.4 - - - -
106D PHE* 6.1 0.4 - - + -
108D ALA* 4.2 1.6 - - + +
109D ARG* 1.3 74.8 - - - +
111D LEU* 1.3 63.4 + - - +
112D SER 3.7 2.0 + - - +
127D HIS 3.3 26.7 - - - +
128D ILE* 4.4 12.1 - - + -
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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