Contacts of the helix formed by residues 128 - 146 (chain B) in PDB entry 2R8J
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 LEU 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 3.6 27.4 - - + -
55B GLN* 5.4 3.6 - - - +
60B ILE* 5.4 1.3 - - + -
92B THR* 5.2 2.2 - - + -
126B VAL* 4.1 19.9 + - + +
127B SER* 1.3 75.8 + - - +
129B GLU* 1.3 65.8 + - - +
130B PRO* 3.3 3.6 - - - -
131B TYR* 3.1 20.3 + - + +
132B ARG* 3.1 38.5 + - + +
154B ILE* 5.6 1.6 - - + -
13P G 4.3 30.3 - - + +
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 5.8 0.3 - - - -
102B TRP* 3.0 36.4 + - + +
127B SER* 3.3 6.8 + - - +
128B LEU* 1.3 76.4 - - - +
130B PRO* 1.3 72.2 - - + +
132B ARG* 2.9 22.1 + - + +
133B ARG* 2.7 64.1 + - + +
425B SER* 2.8 35.4 + - - +
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Residues in contact with PRO 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 5.8 1.6 - - + -
93B ALA* 4.2 7.9 - - + -
102B TRP* 4.0 26.7 - - + -
104B TYR* 3.4 30.3 - - + +
127B SER* 3.5 14.6 - - - +
128B LEU* 3.3 5.2 - - - -
129B GLU* 1.3 93.5 - - + +
131B TYR* 1.3 68.5 + - + +
133B ARG* 3.3 9.3 + - + +
134B GLU* 3.1 28.1 + - - +
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Residues in contact with TYR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 3.6 10.7 - - + -
35B PHE* 3.3 69.1 - + + -
38B VAL* 3.1 36.6 - - + -
39B GLU* 2.8 21.4 + - - -
53B CYS* 3.3 6.5 - - - -
92B THR* 3.2 29.6 - - + +
93B ALA 5.5 0.4 - - - -
104B TYR* 4.3 3.7 + - - -
127B SER 4.2 5.4 - - - -
128B LEU* 3.1 30.4 + - + +
130B PRO* 1.3 76.5 - - + +
132B ARG* 1.3 60.3 + - - +
134B GLU* 3.3 4.1 + - - +
135B SER* 2.9 29.1 + - - -
154B ILE* 4.1 5.2 - - + -
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B SER* 5.6 0.6 + - - -
128B LEU* 3.1 22.8 + - + +
129B GLU* 2.9 32.6 + - - +
131B TYR* 1.3 75.5 - - - +
133B ARG* 1.3 62.1 + - + +
135B SER* 3.4 8.8 - - - -
136B ARG* 3.3 21.3 + - - +
151B ARG* 4.6 5.8 + - - +
154B ILE* 3.9 18.8 - - + -
422B GLU* 4.8 9.9 - - - +
425B SER* 3.7 17.0 + - - -
426B ARG* 3.4 40.3 - - - +
429B ASP* 4.1 33.3 - - - +
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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
----------------------------------------------------------
196A GLY 5.5 5.8 - - - +
197A GLY 3.1 27.3 + - - -
198A ASN* 4.3 19.3 - - - +
199A TYR 5.5 1.0 + - - -
102B TRP* 6.0 1.3 - - + -
129B GLU* 2.7 50.7 + - + +
130B PRO* 3.3 11.4 - - + +
132B ARG* 1.3 73.4 - - + +
134B GLU* 1.3 71.1 + - - +
136B ARG* 2.9 23.6 + - - +
137B LYS* 3.3 13.2 + - - +
428B GLN* 4.8 18.5 + - - +
429B ASP* 5.6 1.1 - - - -
432B GLN* 5.6 4.9 + - - +
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 4.0 9.5 - - + -
38B VAL* 4.1 10.5 - - + -
130B PRO 3.1 16.1 + - - +
131B TYR 3.8 4.0 - - - +
133B ARG* 1.3 83.0 - - - +
135B SER* 1.3 62.1 + - - +
137B LYS* 2.9 55.2 + - - +
138B ALA* 3.4 12.5 + - - +
256B LEU* 4.5 7.4 - - - +
258B TYR* 2.6 46.7 + - + +
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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
----------------------------------------------------------
31B MET* 5.6 0.4 - - - -
34B PHE* 3.8 8.5 - - - -
131B TYR 2.9 18.1 + - - -
132B ARG 3.4 9.0 - - - -
133B ARG 3.1 0.4 - - - -
134B GLU* 1.3 76.0 - - - +
136B ARG* 1.3 61.2 + - - +
138B ALA* 3.4 8.5 + - - +
139B LEU* 3.2 19.8 + - - +
151B ARG* 2.9 30.8 + - - -
154B ILE* 2.8 30.0 + - - -
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ARG 3.3 6.5 + - - +
133B ARG* 2.9 13.3 + - - +
135B SER* 1.3 78.6 - - - +
137B LYS* 1.3 65.2 + - + +
139B LEU* 3.2 15.1 + - + +
140B LYS* 3.0 40.1 + - + +
151B ARG* 3.0 41.5 - - - +
389B ARG* 5.3 0.8 - - - +
429B ASP* 2.9 47.3 + - - +
430B LEU* 4.7 1.0 - - - +
432B GLN* 3.7 21.8 - - + +
433B GLU* 2.8 47.6 + - - +
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Residues in contact with LYS 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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195A ILE* 3.2 46.7 - - + +
196A GLY* 4.0 18.8 - - - +
133B ARG* 3.3 12.8 + - - +
134B GLU* 2.9 41.9 + - - +
136B ARG* 1.3 78.8 - - + +
138B ALA* 1.3 62.5 + - - +
140B LYS* 3.6 7.8 + - - +
141B ILE* 3.3 26.3 + - - +
256B LEU* 3.8 20.1 - - + +
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Residues in contact with ALA 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 MET* 3.8 28.9 - - + -
134B GLU 3.4 4.6 + - - +
135B SER* 3.6 9.4 - - - +
136B ARG 3.2 0.4 - - - -
137B LYS* 1.3 76.8 - - - +
139B LEU* 1.3 60.3 + - - +
141B ILE* 3.1 8.2 + - - +
142B PHE* 2.8 47.9 + - + -
252B ILE* 4.5 6.9 - - + +
256B LEU* 3.8 11.8 - - + +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER 3.2 11.1 + - - +
136B ARG* 3.5 23.8 - - - +
138B ALA* 1.3 78.6 - - - +
140B LYS* 1.3 57.2 + - + +
142B PHE* 2.7 25.7 + - + +
143B LYS* 2.9 44.1 + - - +
149B VAL* 3.7 30.1 - - + -
151B ARG* 3.8 35.7 - - + +
157B VAL* 4.1 17.3 - - + -
433B GLU* 5.1 4.5 - - + +
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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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10A ILE* 5.7 0.4 - - - -
171A PHE* 3.9 5.3 - - - -
194A PHE* 2.8 55.2 + - + +
195A ILE* 4.5 13.1 + - + +
197A GLY* 3.6 10.9 - - - -
199A TYR* 2.7 32.6 + - - -
136B ARG* 3.0 32.2 + - + +
137B LYS* 3.8 5.6 - - - +
139B LEU* 1.3 76.0 - - + +
141B ILE* 1.3 61.7 + - - +
143B LYS* 3.7 8.4 + - - +
144B SER* 3.2 21.7 + - - -
432B GLN* 4.3 11.6 + - - -
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Residues in contact with ILE 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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171A PHE* 4.0 18.6 - - + -
195A ILE* 4.2 7.9 - - + -
137B LYS 3.3 14.8 + - - +
138B ALA 3.1 8.0 + - - +
139B LEU 3.1 0.8 - - - -
140B LYS* 1.3 75.1 - - - +
142B PHE* 1.3 66.1 + - - +
144B SER* 2.6 25.8 + - - +
145B ALA* 3.5 6.9 + - + +
248B ILE* 5.0 5.3 - - + +
251B SER* 4.2 18.4 - - - -
252B ILE* 4.1 22.4 - - + -
255B ILE* 3.4 42.8 - - + -
256B LEU* 4.3 14.6 - - + -
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Residues in contact with PHE 142 (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 ILE* 3.4 42.0 - - + -
31B MET* 5.9 3.1 - - + -
138B ALA* 2.8 31.7 + - + -
139B LEU* 2.7 12.8 + - - +
141B ILE* 1.3 77.1 - - - +
143B LYS* 1.3 63.1 + - - +
145B ALA* 2.9 15.1 + - - +
146B CYS* 3.1 14.4 + - - +
149B VAL* 3.9 17.5 - - + -
157B VAL* 3.6 32.8 - - + -
159B LEU* 4.2 11.3 - - + +
248B ILE* 3.7 20.0 - - + +
252B ILE* 3.1 33.0 - - + -
260B THR* 5.7 0.4 - - + -
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Residues in contact with LYS 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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167A ASN* 4.6 4.3 + - - +
139B LEU* 2.9 53.6 + - + +
140B LYS* 4.1 7.2 - - - +
142B PHE* 1.3 72.3 - - - +
144B SER* 1.3 60.2 + - - +
146B CYS 3.0 25.4 + - - +
147B ASP* 5.0 0.3 - - - -
149B VAL* 3.8 22.0 - - + -
432B GLN 5.6 1.6 + - - -
433B GLU* 5.0 17.4 + - - +
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Residues in contact with SER 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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166A PHE* 6.3 0.2 - - - -
167A ASN* 3.1 38.7 + - - +
171A PHE* 3.4 41.4 - - - +
140B LYS 3.2 9.9 + - - -
141B ILE* 2.6 21.8 + - - +
142B PHE 3.1 0.8 - - - -
143B LYS* 1.3 76.1 - - - +
145B ALA* 1.3 58.6 + - - +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ILE* 4.1 7.2 - - + +
142B PHE 2.9 7.0 + - - +
144B SER* 1.3 82.0 + - - +
146B CYS* 1.3 58.2 + - - +
164B ILE* 3.2 24.1 - - - +
244B VAL* 5.2 0.2 - - - +
248B ILE* 3.7 33.8 - - + +
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Residues in contact with CYS 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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142B PHE 3.1 9.8 + - - +
143B LYS* 3.0 25.0 + - - +
144B SER 3.6 0.2 - - - -
145B ALA* 1.3 82.5 - - - +
147B ASP* 1.3 62.7 + - - +
148B LEU 3.0 26.2 + - - -
149B VAL* 3.7 3.7 + - + +
159B LEU* 3.9 24.7 - - + -
160B ASP 3.4 32.8 - - - -
161B LEU* 4.4 6.7 - - + -
164B ILE* 4.5 6.1 - - + -
248B ILE* 5.0 2.7 - - + -
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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
------------------------------------------------------------
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