Contacts of the strand formed by residues 123 - 133 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B ASP* 4.6 2.6 - - - +
122B ASP* 1.3 74.1 + - - +
124B GLN* 1.3 78.5 + - - +
160B TRP* 4.8 0.2 - - - -
189B ARG* 6.6 0.2 - - - -
190B ILE 3.2 9.6 - - - -
191B SER* 3.0 28.3 - - - +
192B ARG 4.6 0.2 - - - +
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Residues in contact with GLN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PRO 4.6 1.4 - - - +
114B LEU* 3.3 29.9 - - + +
115B ASP* 2.9 46.3 + - - +
116B PHE* 4.9 1.0 - - - +
122B ASP* 2.7 24.4 + - - -
123B SER* 1.3 81.9 + - - +
125B THR* 1.3 65.0 + - - +
126B LEU* 3.9 1.3 - - + -
160B TRP* 3.8 22.6 - - + -
189B ARG* 3.2 7.8 - - - +
190B ILE* 2.7 49.5 + - + +
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B SER* 3.7 4.7 + - - -
113B PRO 4.6 4.8 - - - +
124B GLN* 1.3 73.4 + - - +
126B LEU* 1.3 69.5 + - - +
127B HIS* 3.4 35.5 + - + +
187B GLN* 4.3 9.2 - - + +
188B LEU 3.6 3.6 - - - +
189B ARG* 3.3 39.3 + - + +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.2 7.4 - - + -
36B THR 6.0 0.2 - - - +
37B PHE* 3.7 42.4 - - + -
112B SER* 3.6 9.0 - - - +
114B LEU* 3.6 32.1 - - + -
124B GLN* 4.7 1.3 - - + -
125B THR* 1.3 79.6 - - - +
127B HIS* 1.3 62.4 + - - +
128B ILE* 4.4 0.4 - - - -
157B LEU* 4.8 4.0 - - + -
187B GLN* 3.5 6.4 - - - -
188B LEU* 2.6 63.8 + - + +
190B ILE* 3.8 28.9 - - + -
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Residues in contact with HIS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 4.8 0.2 - - - -
80B ASN* 2.6 33.3 + - - +
110B VAL* 3.3 8.8 - - - +
112B SER* 3.6 15.4 + - - +
113B PRO* 5.5 5.2 - - + -
125B THR* 3.4 37.5 + - + +
126B LEU* 1.3 76.5 + - - +
128B ILE* 1.3 58.4 + - - +
129B TYR* 3.4 31.4 + - + -
185B ASP* 3.2 32.0 + - - -
186B TYR 3.4 2.5 - - - -
187B GLN* 3.7 15.0 - - + +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE* 4.1 10.3 - - + +
24B LEU* 4.4 3.8 - - + -
37B PHE* 4.1 20.0 - - + -
39B VAL* 4.3 29.6 - - + -
78B PHE* 3.3 37.5 - - + -
80B ASN* 3.8 3.4 - - - +
81B VAL* 5.9 0.4 - - + -
106B PHE* 5.3 2.9 - - + -
110B VAL* 4.4 12.6 - - + -
126B LEU 5.7 0.7 - - - -
127B HIS* 1.3 76.4 - - - +
129B TYR* 1.3 60.2 + - - +
130B LEU 3.7 1.9 + - - -
165B PHE* 4.3 24.2 - - + -
186B TYR* 2.9 41.4 + - + +
188B LEU* 5.8 3.4 - - + -
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Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASP* 3.7 21.5 - - - -
78B PHE* 3.4 8.4 - - - -
79B VAL* 2.8 51.2 + - + -
80B ASN* 2.9 23.0 + - + +
127B HIS* 3.4 50.5 + + + -
128B ILE* 1.3 74.6 - - - +
130B LEU* 1.3 58.8 + - - +
183B LYS* 3.5 26.2 - - - -
184B LEU 3.6 7.0 - - - +
185B ASP* 3.4 28.6 + - + -
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 4.1 18.2 - - + -
22B ILE* 3.9 13.9 - - + -
43B LEU* 4.0 16.2 - - + -
76B ILE* 3.3 29.6 - - + -
77B ARG 3.9 4.9 - - - +
78B PHE* 3.8 32.8 - - + -
79B VAL* 4.4 0.4 - - - -
128B ILE 3.7 2.0 + - - -
129B TYR* 1.3 71.7 - - - +
131B ILE* 1.3 60.9 + - - +
142B LEU* 3.6 7.4 - - + +
183B LYS* 3.3 3.8 - - - +
184B LEU* 2.7 46.7 + - + +
186B TYR* 3.6 25.8 - - + -
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ARG* 5.7 1.8 - - - +
76B ILE* 3.5 9.2 - - - +
77B ARG* 2.9 56.9 + - + +
78B PHE 5.6 0.2 - - - -
79B VAL* 3.8 24.5 - - + -
130B LEU* 1.3 72.5 - - - +
132B VAL* 1.3 68.8 + - - +
142B LEU* 3.8 3.8 - - - +
174B PHE* 4.4 12.1 - - + -
176B LEU* 5.5 2.2 - - + -
181B GLU* 3.5 39.0 - - + +
182B SER 3.4 13.0 - - - +
183B LYS* 3.8 21.8 - - + -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B PRO* 4.6 1.3 - - + -
75B GLU 3.3 25.4 - - - +
76B ILE* 3.8 11.2 - - + -
131B ILE* 1.3 76.8 - - - +
133B ARG* 1.3 74.2 + - - +
134B SER* 3.8 1.2 + - - -
140B ILE* 4.1 32.8 - - + +
142B LEU* 3.3 33.4 - - + -
181B GLU* 3.5 6.1 - - - -
182B SER* 3.1 34.8 + - - +
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 4.6 5.7 - - - -
90A VAL* 3.8 23.3 - - + -
91A ASP* 5.5 6.1 - - - +
103A LEU* 3.7 21.6 - - - +
75B GLU* 3.9 12.7 + - - +
77B ARG* 4.2 15.8 - - - +
131B ILE* 4.8 0.2 - - - +
132B VAL* 1.3 85.1 - - - +
134B SER* 1.3 71.5 + - - +
135B VAL* 3.8 5.2 + - - +
140B ILE* 4.3 5.7 - - - +
176B LEU* 3.1 22.2 + - - +
177B GLU* 3.1 31.3 + - - +
179B ARG* 3.6 29.5 + - - +
180B LEU 4.0 2.7 - - - +
181B GLU* 2.8 44.4 + - - +
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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