Contacts of the strand formed by residues 133 - 147 (chain B) in PDB entry 6J8J
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 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B LEU* 3.6 26.3 - - + +
127B LEU 3.5 7.2 - - - +
128B PHE* 3.7 29.3 - - + -
129B PHE 6.0 0.2 - - - +
131B ASN 4.3 1.7 + - - -
132B TYR* 1.3 89.2 - - - +
134B HIS* 1.3 59.7 + - - +
135B ASN 4.3 0.7 + - - -
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Residues in contact with HIS 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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278A ASN* 5.3 2.9 + - + -
326A GLU* 3.2 9.7 - - + +
327A GLY* 2.8 44.0 + - - -
125B ARG 3.2 4.3 - - - +
126B LEU* 3.7 5.2 - - - +
127B LEU* 3.0 36.3 + - + +
129B PHE* 4.1 19.5 - - + -
132B TYR* 3.9 16.0 + - + -
133B GLU* 1.3 74.6 + - - +
135B ASN* 1.3 73.6 + - - +
136B THR* 3.7 21.9 + - + +
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Residues in contact with ASN 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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124B TYR* 4.7 0.7 - - - +
125B ARG 3.6 13.0 + - - +
126B LEU* 4.7 12.4 - - + +
133B GLU 4.3 0.8 + - - -
134B HIS* 1.3 86.8 + - - +
136B THR* 1.3 68.2 + - - +
304B NAG 1.5 74.3 + - + +
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLU* 3.8 31.6 + - + +
123B VAL 3.4 10.3 - - - +
124B TYR* 3.6 4.2 - - - -
125B ARG* 3.4 30.0 + - - +
127B LEU* 4.2 7.8 - - - +
134B HIS* 3.7 20.9 - - - +
135B ASN* 1.3 82.1 + - - +
137B SER* 1.3 70.8 + - - +
138B VAL* 5.7 3.4 - - + -
304B NAG 5.0 1.6 - - - -
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Residues in contact with SER 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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122B HIS* 5.3 1.2 - - - +
123B VAL 3.4 5.4 - - - -
124B TYR* 4.1 22.9 - - - -
136B THR* 1.3 84.1 - - - +
138B VAL* 1.3 64.2 + - - +
139B VAL* 4.3 13.0 - - - +
304B NAG 4.4 8.3 - - - -
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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
----------------------------------------------------------
326A GLU* 6.0 1.8 - - - +
42B SER* 4.6 16.2 - - - +
122B HIS* 3.6 1.6 - - - +
123B VAL* 3.1 51.9 + - + +
125B ARG* 5.1 7.9 - - + +
136B THR* 5.7 4.0 - - + +
137B SER* 1.3 76.0 + - - +
139B VAL* 1.3 74.5 + - - +
140B LYS* 4.8 14.6 - - + -
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Residues in contact with VAL 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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120B GLU* 4.5 3.6 - - - +
121B CYS 3.7 3.8 - - - +
122B HIS* 3.2 36.1 - - + +
137B SER* 4.3 12.6 - - - +
138B VAL* 1.3 82.1 - - - +
140B LYS* 1.3 68.9 + - - +
141B LYS* 4.2 21.5 + - - +
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Residues in contact with LYS 140 (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 GLU* 2.4 37.9 + - - +
24B VAL 5.6 2.4 + - - +
25B ASP* 4.5 14.0 + - - +
40B CYS* 3.7 30.5 - - + -
41B ILE 3.6 19.3 + - - +
42B SER* 5.2 5.4 - - - +
119B TYR 4.1 0.7 - - - +
120B GLU* 3.7 0.9 - - - -
121B CYS* 2.9 34.1 + - - +
123B VAL* 5.8 1.6 - - + -
138B VAL* 4.3 14.3 + - + +
139B VAL* 1.3 78.6 - - - +
141B LYS* 1.3 62.9 + - - +
142B ILE* 4.1 5.0 + - + +
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Residues in contact with LYS 141 (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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119B TYR 3.5 7.4 - - - +
120B GLU* 3.4 34.8 + - + +
139B VAL* 4.5 15.1 - - - +
140B LYS* 1.3 74.1 - - - +
142B ILE* 1.3 65.3 + - - +
143B HIS 4.4 0.2 + - - -
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Residues in contact with ILE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER* 2.4 43.3 - - - +
27B GLU 5.0 0.4 - - - +
28B THR* 5.4 3.1 - - + -
38B ILE* 3.2 20.4 - - + -
39B LEU 4.6 7.4 - - - +
40B CYS* 5.2 2.9 - - + -
57B TRP* 2.9 42.0 - - + -
118B ASP* 4.8 0.9 - - - -
119B TYR* 2.7 54.7 + - + +
140B LYS* 4.6 7.2 - - + +
141B LYS* 1.3 79.9 - - - +
143B HIS* 1.3 58.3 + - - +
144B ILE* 4.7 5.6 - - + -
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Residues in contact with HIS 143 (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 THR* 2.7 42.0 - - + +
62B LYS* 4.4 22.3 + - + +
117B GLY* 3.1 29.4 - - - -
118B ASP* 3.3 22.2 - - - +
141B LYS 4.3 0.2 - - - -
142B ILE* 1.3 72.6 - - - +
144B ILE* 1.3 66.2 + - - +
145B GLU* 4.5 12.2 - - + +
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Residues in contact with ILE 144 (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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26B SER* 4.9 6.1 - - - +
27B GLU 4.0 18.4 - - - +
28B THR 3.7 9.0 - - - +
30B ALA* 4.8 13.2 - - + -
36B PHE* 4.3 18.4 - - + -
38B ILE* 4.9 7.9 - - + -
108B ILE* 5.8 2.7 - - + -
111B VAL* 5.9 2.0 - - + -
115B HIS* 3.2 26.7 - - + +
116B SER* 3.5 2.0 + - - -
117B GLY 3.0 30.2 + - - +
119B TYR* 3.6 32.1 - - + +
142B ILE* 4.2 4.5 + - + -
143B HIS* 1.3 87.7 + - - +
145B GLU* 1.3 60.0 + - - +
146B VAL* 4.6 8.5 - - + -
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Residues in contact with GLU 145 (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 THR 3.2 13.0 + - - +
29B GLU* 3.8 5.0 - - + +
30B ALA 3.5 17.1 + - - -
62B LYS* 3.1 36.4 + - - +
116B SER* 4.0 5.6 - - - +
143B HIS* 4.5 11.7 + - + +
144B ILE* 1.3 75.1 - - - +
146B VAL* 1.3 74.9 + - - +
147B VAL* 4.0 9.6 - - + +
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Residues in contact with VAL 146 (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 ALA* 3.4 15.5 - - + +
32B TYR* 4.0 15.0 - - + +
111B VAL* 4.3 11.0 - - + -
112B THR 3.6 16.6 - - - +
113B TYR* 3.5 35.9 - - + -
115B HIS 3.6 24.0 - - - +
116B SER* 4.0 11.7 + - - -
144B ILE* 4.6 4.5 - - + -
145B GLU* 1.3 83.1 - - - +
147B VAL* 1.3 75.3 + - - +
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Residues in contact with VAL 147 (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 GLU* 4.7 17.7 - - + -
30B ALA 2.7 24.0 + - - +
31B VAL* 3.3 2.7 - - + -
32B TYR* 2.9 24.1 + - - -
113B TYR* 4.9 2.0 - - - -
145B GLU* 4.0 14.6 - - + +
146B VAL* 1.3 85.9 - - - +
148B ASP* 1.3 59.2 + - - +
149B LYS 3.7 24.2 - - - +
150B ALA* 4.6 3.6 - - - +
151B ASN* 4.4 9.6 - - - +
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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