Contacts of the strand formed by residues 125 - 139 (chain B) in PDB entry 5J0B
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 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B PHE* 3.7 34.5 - - + -
45B HIS* 4.3 0.7 - - + -
46B PRO* 4.1 14.8 - - + +
48B PRO* 3.8 17.0 - - - +
51B ASP* 3.1 15.8 + - - +
120B MET* 3.6 15.1 - - + +
121B GLU* 3.4 1.6 - - - -
122B ARG* 2.6 47.5 + - - -
124B SER* 1.3 74.9 - - - +
126B LYS* 1.3 58.3 + - - +
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Residues in contact with LYS 126 (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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21B PHE* 4.9 3.6 - - - -
119B ARG* 3.7 27.1 - - - +
120B MET* 3.4 5.6 - - - +
121B GLU* 4.0 24.4 + - + -
123B GLY 3.4 20.9 - - - +
124B SER* 3.3 10.9 + - - +
125B THR* 1.3 80.7 - - - +
127B TYR* 1.3 68.3 - - - +
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Residues in contact with TYR 127 (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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19B THR 5.8 2.5 + - - -
21B PHE* 3.5 54.6 + + + +
119B ARG* 3.4 6.1 - - - +
120B MET* 3.0 37.9 + - + +
126B LYS* 1.3 78.2 - - - +
128B SER* 1.3 76.6 + - - +
129B TYR* 3.7 39.7 + + - -
130B LYS 5.2 0.2 - - - -
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Residues in contact with SER 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.6 11.1 - - - +
117B PHE* 3.9 18.8 - - - -
118B PHE 3.7 4.5 - - - -
119B ARG* 2.7 39.5 + - - +
127B TYR* 1.3 81.4 - - - +
129B TYR* 1.3 60.8 + - - +
130B LYS* 2.9 25.3 + - - +
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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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21B PHE* 3.8 4.8 - - + -
22B TRP* 3.5 33.7 - - - -
23B LEU* 3.5 31.0 - - + -
43B PHE* 3.5 26.9 - + + -
44B PHE 2.6 21.4 + - - -
45B HIS* 3.9 0.5 - - - +
117B PHE* 3.4 19.2 - - - +
118B PHE* 2.8 34.4 + + - +
120B MET* 3.7 28.1 - - + +
127B TYR* 3.7 30.1 - + - -
128B SER* 1.3 68.3 - - - +
130B LYS* 1.3 59.3 + - - +
131B SER 3.1 14.7 + - - +
132B PRO 4.1 5.9 - - - +
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 3.8 12.7 + - - -
65B ALA 4.8 3.2 + - - -
117B PHE* 3.3 38.0 - - + -
127B TYR* 5.2 0.8 - - - -
128B SER* 2.9 32.9 + - - +
129B TYR* 1.3 70.6 - - - +
131B SER* 1.3 62.0 + - - +
133B GLN* 3.2 35.1 + - - +
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Residues in contact with SER 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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22B TRP* 5.8 0.7 - - - -
23B LEU 5.0 3.1 + - - -
129B TYR* 3.1 11.9 - - - +
130B LYS* 1.3 81.8 - - - +
132B PRO* 1.3 73.8 - - - +
133B GLN 4.1 0.2 - - - +
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Residues in contact with PRO 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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23B LEU* 3.2 52.9 - - + +
24B GLN* 4.8 0.7 - - - -
25B VAL* 4.1 16.0 - - + +
27B GLU* 4.3 25.6 - - + +
117B PHE* 5.4 1.2 - - - -
118B PHE 5.8 0.3 + - - -
129B TYR* 4.1 8.3 - - - +
131B SER* 1.3 92.8 - - - +
133B GLN* 1.3 60.4 + - - +
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Residues in contact with GLN 133 (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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25B VAL* 4.6 3.6 - - - -
26B GLN 4.2 0.3 - - - +
27B GLU* 3.5 25.3 - - - +
60B TRP* 6.2 0.2 - - - -
63B GLU* 3.4 32.4 + - - +
115B SER* 3.4 27.3 - - - +
116B TYR 3.3 11.7 - - - +
117B PHE* 4.0 19.4 - - + +
130B LYS* 3.2 43.1 + - - +
131B SER* 4.1 0.4 - - - +
132B PRO* 1.3 75.6 - - - +
134B LEU* 1.3 61.1 + - - +
135B SER* 3.8 2.2 + - - +
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Residues in contact with LEU 134 (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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25B VAL* 4.3 5.5 - - + +
26B GLN* 3.1 29.6 - - + +
27B GLU 4.1 0.4 - - - -
28B SER 4.4 0.2 - - - +
29B VAL* 3.9 21.3 - - + +
39B VAL* 3.8 35.4 - - + -
60B TRP* 4.4 18.3 - - + -
103B LEU* 3.9 28.7 - - + -
105B ILE* 5.8 0.2 - - + -
114B GLY 3.7 1.4 - - - +
115B SER* 3.2 2.5 - - - -
116B TYR* 2.9 43.1 + - + +
133B GLN* 1.3 71.0 - - - +
135B SER* 1.3 63.6 + - - +
136B VAL* 3.7 12.4 + - + -
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Residues in contact with SER 135 (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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27B GLU 2.9 21.0 + - - -
28B SER* 3.3 3.0 - - - -
29B VAL* 2.9 29.6 + - - +
114B GLY 3.6 6.3 - - - -
115B SER* 3.3 16.5 + - - -
133B GLN* 3.8 1.8 + - - +
134B LEU* 1.3 70.7 - - - +
136B VAL* 1.3 61.4 + - - +
137B HIS* 3.8 23.0 - - - -
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Residues in contact with VAL 136 (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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29B VAL* 3.7 20.0 - - + -
31B VAL* 4.7 9.0 - - + -
37B VAL* 6.4 0.2 - - + -
105B ILE* 4.2 25.1 - - + -
112B ASP* 3.8 19.5 - - + +
113B ASN* 3.2 7.1 - - - +
114B GLY 2.9 33.2 + - - +
116B TYR* 3.7 22.0 - - + -
134B LEU* 4.3 10.5 - - + -
135B SER* 1.3 75.1 - - - +
137B HIS* 1.3 66.8 + - - +
138B VAL* 3.9 18.6 - - + -
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Residues in contact with HIS 137 (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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28B SER* 3.4 24.8 + - - -
29B VAL 3.0 11.1 + - - +
30B THR* 3.3 17.4 - - + +
31B VAL* 3.1 24.9 + - - +
113B ASN* 3.3 10.7 + - - +
135B SER* 3.8 22.3 - - - -
136B VAL* 1.3 77.1 + - - +
138B VAL* 1.3 62.4 + - - +
139B THR* 4.8 4.7 - - + -
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Residues in contact with VAL 138 (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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31B VAL* 3.2 20.2 - - + +
33B GLU* 3.9 23.1 - - + -
108B ALA* 4.4 6.5 - - + -
109B ARG 3.2 36.1 - - - +
110B ARG* 3.2 26.0 + - + +
112B ASP* 4.0 8.3 - - + -
113B ASN* 2.5 27.5 + - - +
136B VAL* 3.9 18.2 - - + -
137B HIS* 1.3 73.2 - - - +
139B THR* 1.3 61.1 + - - +
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Residues in contact with THR 139 (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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30B THR* 3.8 26.1 - - + +
31B VAL 3.1 6.1 + - - -
32B GLN* 3.7 21.8 - - - +
33B GLU* 2.8 30.7 + - - +
110B ARG* 3.7 5.1 + - - +
137B HIS* 4.5 6.7 - - + +
138B VAL* 1.3 76.2 - - - +
140B ASP* 1.3 61.8 + - - +
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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