Contacts of the strand formed by residues 123 - 133 (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 SER 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115D ASP* 4.6 2.6 - - - +
118D ARG* 6.1 0.4 - - - +
121D PHE 5.3 0.3 + - - -
122D ASP* 1.3 74.4 + - - +
124D GLN* 1.3 80.9 + - - +
160D TRP* 4.8 0.2 - - - -
163D GLU* 5.1 0.2 + - - -
189D ARG* 6.5 0.4 - - - -
190D ILE 3.2 9.0 - - - -
191D SER* 3.0 29.1 - - - +
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Residues in contact with GLN 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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113D PRO 4.6 1.0 - - - +
114D LEU* 3.4 29.3 - - + +
115D ASP* 2.9 46.2 + - - +
116D PHE* 4.9 0.6 - - - +
122D ASP* 2.7 24.9 + - - -
123D SER* 1.3 82.8 + - - +
125D THR* 1.3 67.2 + - - +
126D LEU* 3.9 1.6 - - + -
160D TRP* 3.8 22.4 - - + -
189D ARG* 3.2 7.7 - - - +
190D ILE* 2.6 50.6 + - + +
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Residues in contact with THR 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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112D SER* 3.7 4.7 + - - -
113D PRO 4.6 4.4 - - - +
124D GLN* 1.3 74.4 + - - +
126D LEU* 1.3 68.9 + - - +
127D HIS* 3.3 35.3 - - + +
187D GLN* 4.3 9.4 - - + +
188D LEU 3.7 3.4 - - - +
189D ARG* 3.4 39.4 + - + +
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Residues in contact with LEU 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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30D LEU* 4.2 11.4 - - + -
36D THR 6.0 0.2 - - - +
37D PHE* 3.7 42.2 - - + -
112D SER* 3.6 9.9 - - - +
114D LEU* 3.6 30.7 - - + -
124D GLN* 4.7 1.3 - - + -
125D THR* 1.3 79.5 - - - +
127D HIS* 1.3 62.0 + - - +
128D ILE* 5.7 0.2 - - - -
157D LEU* 4.8 3.4 - - + -
187D GLN* 3.5 6.6 - - - -
188D LEU* 2.6 64.6 + - + +
190D ILE* 3.8 25.1 - - + -
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Residues in contact with HIS 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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37D PHE* 4.7 0.4 - - - -
80D ASN* 2.6 31.9 + - - +
110D VAL* 3.3 8.7 - - - +
112D SER* 3.6 14.7 + - - +
113D PRO* 5.5 5.8 - - + -
125D THR* 3.3 38.1 + - + +
126D LEU* 1.3 75.3 + - - +
128D ILE* 1.3 58.7 + - - +
129D TYR* 3.4 29.8 + - + -
185D ASP* 3.2 31.8 + - - -
186D TYR 3.4 2.0 - - - -
187D GLN* 3.7 15.9 - - + +
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Residues in contact with ILE 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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22D ILE* 4.1 10.0 - - + +
24D LEU* 4.4 4.3 - - + -
37D PHE* 4.1 19.7 - - + -
39D VAL* 4.3 30.1 - - + -
78D PHE* 3.3 37.7 - - + -
80D ASN* 3.8 3.4 - - - +
81D VAL* 5.9 0.7 - - + -
106D PHE* 5.3 2.2 - - + -
110D VAL* 4.4 12.1 - - + -
126D LEU 5.7 0.2 - - - -
127D HIS* 1.3 76.3 - - - +
129D TYR* 1.3 60.6 + - - +
130D LEU 3.7 1.7 + - - -
165D PHE* 4.3 23.3 - - + -
186D TYR* 2.9 41.4 + - + +
188D LEU* 5.8 4.0 - - + -
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Residues in contact with TYR 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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154C ASP* 3.6 22.9 - - - -
78D PHE* 3.4 8.1 - - - -
79D VAL* 2.8 49.4 + - + -
80D ASN* 2.9 25.1 + - + +
127D HIS* 3.4 39.0 + + + -
128D ILE* 1.3 74.6 - - - +
130D LEU* 1.3 59.0 + - - +
183D LYS* 3.5 24.9 - - - -
184D LEU 3.6 7.4 - - - +
185D ASP* 3.4 36.9 + - + -
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Residues in contact with LEU 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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20D THR* 4.1 19.5 - - + +
22D ILE* 3.9 13.0 - - + -
43D LEU* 4.0 16.6 - - + -
76D ILE* 3.3 28.9 - - + -
77D ARG 3.9 5.4 - - - +
78D PHE* 3.7 32.5 - - + -
79D VAL* 4.4 0.2 - - - -
85D ARG* 5.3 0.2 - - - +
128D ILE 3.7 2.2 + - - -
129D TYR* 1.3 72.9 - - - +
131D ILE* 1.3 61.2 + - - +
142D LEU* 3.6 7.4 - - + +
183D LYS* 3.2 3.8 - - - +
184D LEU* 2.7 45.6 + - + +
186D TYR* 3.6 26.0 - - + -
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Residues in contact with ILE 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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105C ARG* 5.7 2.2 - - - +
76D ILE* 3.5 9.5 - - - +
77D ARG* 2.9 54.9 + - + +
78D PHE 5.6 0.4 - - - -
79D VAL* 3.8 25.1 - - + -
130D LEU* 1.3 73.3 - - - +
132D VAL* 1.3 69.3 + - - +
142D LEU* 3.8 3.1 - - - +
174D PHE* 4.4 12.6 - - + -
176D LEU* 5.5 1.8 - - + -
181D GLU* 3.5 38.6 - - + +
182D SER 3.4 12.6 - - - +
183D LYS* 3.8 22.2 - - + -
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Residues in contact with VAL 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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74D PRO* 4.6 1.3 - - + -
75D GLU 3.3 24.5 - - - +
76D ILE* 3.8 11.2 - - + -
131D ILE* 1.3 78.3 - - - +
133D ARG* 1.3 72.4 + - - +
134D SER* 3.8 1.2 + - - -
140D ILE* 4.1 33.9 - - + +
142D LEU* 3.3 33.2 - - + -
181D GLU* 3.5 6.1 - - - -
182D SER* 3.1 34.5 + - - +
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Residues in contact with ARG 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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42C PHE* 4.5 6.3 - - - -
90C VAL* 3.9 23.1 - - + -
91C ASP* 5.5 6.0 - - - +
103C LEU* 3.7 21.8 - - - +
75D GLU* 3.9 13.3 + - - +
77D ARG* 4.2 15.0 - - - +
131D ILE* 4.8 0.2 - - - +
132D VAL* 1.3 84.9 - - - +
134D SER* 1.3 70.9 + - - +
135D VAL* 3.8 2.9 + - - +
140D ILE* 4.2 6.1 - - - +
176D LEU* 3.1 22.0 + - - +
177D GLU* 3.1 30.9 + - - +
179D ARG* 3.6 26.3 + - - +
180D LEU 4.0 2.7 - - - +
181D GLU* 2.8 44.0 + - - +
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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