Contacts of the helix formed by residues 129 - 145 (chain B) in PDB entry 6BJV
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 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLN* 5.6 7.6 - - + +
117A ARG 4.4 11.0 - - - +
118A GLY* 3.9 17.7 + - - +
119A VAL* 4.6 4.0 - - - -
107B GLN* 5.1 0.7 - - - +
125B GLY* 3.6 7.8 - - - -
126B GLY* 2.6 35.2 + - - +
128B ARG* 1.3 80.9 - - + +
130B LEU* 1.3 54.9 + - - +
131B GLN 3.1 3.6 - - - -
132B HIS* 2.7 39.9 + - + +
133B LEU* 2.9 18.0 + - - +
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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
----------------------------------------------------------
63B TRP* 4.0 26.2 - - + -
65B PHE* 4.2 8.1 - - + -
95B VAL* 4.1 9.6 - - + -
96B ASN* 3.5 22.9 - - - +
99B ALA* 3.2 33.2 - - + -
103B LEU* 4.1 10.5 - - + -
110B CYS* 4.5 11.0 - - + -
126B GLY 3.4 2.7 + - - +
127B SER* 3.3 18.9 + - - +
128B ARG 3.3 1.0 - - - -
129B THR* 1.3 77.4 - - - +
131B GLN* 1.3 60.8 + - - +
133B LEU* 4.0 9.2 - - + -
134B CYS* 3.1 26.2 + - - -
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PRO 5.6 4.4 - - - -
96B ASN* 5.0 9.8 + - - +
128B ARG 4.2 16.5 + - - +
130B LEU* 1.3 80.1 - - - +
132B HIS* 1.3 95.0 + - - +
134B CYS* 4.0 3.9 - - - +
135B GLU* 3.5 30.1 + - - +
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Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ARG* 5.7 9.2 + - + -
119A VAL* 3.9 20.8 - - + +
147A LEU* 5.5 4.3 - - + +
148A THR 4.1 13.7 - - - -
149A PRO* 3.4 30.4 - - + +
128B ARG 5.5 0.2 - - - -
129B THR* 2.7 26.8 + - + +
131B GLN* 1.3 106.0 - - + +
133B LEU* 1.3 63.5 + - - +
135B GLU* 3.6 10.8 + - - +
136B MET* 3.2 27.1 + - + +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 3.8 21.3 - - + -
63B TRP* 4.6 11.2 - - + -
110B CYS* 3.9 29.4 - - + +
111B THR 4.9 0.2 - - - +
123B ILE* 3.6 29.8 - - + +
124B SER 3.9 11.4 - - - +
125B GLY* 3.8 21.5 - - - +
126B GLY 4.4 0.7 - - - +
129B THR* 2.9 29.1 + - - +
130B LEU* 3.3 14.1 + - + +
132B HIS* 1.3 74.5 - - - +
134B CYS* 1.3 55.1 + - - +
136B MET* 3.1 3.1 + - - +
137B ALA* 2.5 38.6 + - - +
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Residues in contact with CYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TRP* 3.9 11.0 - - - -
90B TRP* 3.6 14.5 - - + -
92B GLY* 4.9 11.4 - - - -
95B VAL* 3.6 38.6 - - - -
96B ASN* 4.3 7.2 - - - -
130B LEU* 3.1 24.4 + - - +
131B GLN* 4.0 4.7 - - - +
133B LEU* 1.3 77.4 - - - +
135B GLU* 1.3 65.7 + - + +
137B ALA* 3.0 18.2 + - - -
138B ILE* 3.0 15.0 + - - +
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Residues in contact with GLU 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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147A LEU* 5.3 9.4 - - + +
148A THR 4.9 7.6 - - - +
131B GLN* 3.5 20.8 + - - +
132B HIS* 4.2 11.6 - - - +
133B LEU 3.4 0.4 - - - -
134B CYS* 1.3 77.2 - - + +
136B MET* 1.3 54.4 + - - +
138B ILE* 3.1 14.5 - - - +
139B ARG* 2.7 47.0 + - - +
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Residues in contact with MET 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 4.8 5.2 - - + -
121A VAL* 3.8 27.6 - - + -
140A SER* 4.4 7.6 - - - +
143A GLU* 4.1 12.6 - - + +
144A LEU* 4.0 33.9 - - + +
147A LEU* 3.5 32.8 - - + -
123B ILE* 4.5 10.8 - - + -
132B HIS 3.2 17.2 + - - +
133B LEU* 3.1 5.6 + - - +
135B GLU* 1.3 75.9 - - - +
137B ALA* 1.3 63.5 + - - +
138B ILE 3.2 2.0 - - - -
139B ARG* 3.5 7.6 + - + +
140B SER* 3.0 47.7 + - - +
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Residues in contact with ALA 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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63B TRP* 4.2 1.6 - - + -
90B TRP* 3.6 15.4 - - + -
112B TYR* 3.5 39.4 - - + -
123B ILE* 4.2 10.5 - - + +
133B LEU 2.5 21.8 + - - +
134B CYS* 3.6 7.0 - - - +
136B MET* 1.3 72.1 - - - +
138B ILE* 1.3 58.5 + - - +
140B SER* 4.0 0.7 - - - -
141B LYS* 3.0 30.8 + - - +
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Residues in contact with ILE 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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87B LEU* 4.3 32.8 - - + +
90B TRP* 3.7 24.4 - - + +
91B THR* 6.5 0.2 - - - -
134B CYS 3.0 11.7 + - - +
135B GLU* 3.1 27.8 - - - +
137B ALA* 1.3 78.4 - - - +
139B ARG* 1.3 64.8 + - + +
141B LYS* 3.8 5.5 - - + +
142B GLN* 2.9 33.5 + - + +
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Residues in contact with ARG 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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143A GLU* 4.9 24.3 - - + +
146A GLN 5.4 1.0 + - - -
147A LEU* 3.8 28.8 - - - +
135B GLU* 2.7 38.7 + - - +
136B MET* 3.5 16.7 + - - +
138B ILE* 1.3 81.4 - - + +
140B SER* 1.3 65.5 + - - +
142B GLN* 3.2 11.9 + - - +
143B GLU* 2.9 25.5 + - - +
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Residues in contact with SER 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 4.9 2.8 - - - +
136A MET* 3.6 11.6 - - - +
140A SER* 5.0 5.9 + - - -
143A GLU* 6.1 1.3 - - - -
112B TYR* 6.0 0.2 - - - -
114B ILE* 5.6 1.8 - - - -
121B VAL* 4.0 16.4 - - - +
123B ILE* 3.7 25.1 - - - +
136B MET* 3.0 32.5 + - - +
137B ALA 4.0 1.3 - - - -
139B ARG* 1.3 76.0 - - - +
141B LYS* 1.3 63.1 + - - +
143B GLU* 3.2 2.7 + - - -
144B LEU* 2.9 25.6 + - - +
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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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59B PHE* 3.9 17.6 - - - -
61B GLU* 3.1 13.6 + - - +
86B VAL 2.7 22.7 + - - -
87B LEU* 4.2 13.8 + - + +
89B SER* 2.5 30.9 + - - -
90B TRP* 3.8 13.6 - - + +
112B TYR* 3.4 20.2 - - + +
114B ILE* 3.6 22.1 - - + +
137B ALA 3.0 19.7 + - - +
138B ILE* 3.8 7.0 - - + +
140B SER* 1.3 76.7 - - - +
142B GLN* 1.3 64.7 + - - +
143B GLU 3.2 0.5 + - - -
144B LEU* 3.4 2.4 + - - +
145B LEU* 3.2 37.5 + - + +
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Residues in contact with GLN 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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83B LEU* 5.2 0.8 - - + +
87B LEU* 4.1 32.4 - - + +
138B ILE* 2.9 24.4 + - + +
139B ARG* 3.6 11.5 - - - +
141B LYS* 1.3 76.8 - - - +
143B GLU* 1.3 62.4 + - - +
145B LEU* 3.7 2.2 + - - +
146B GLN* 3.4 44.9 + - - +
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Residues in contact with GLU 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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136A MET* 4.1 12.8 - - + -
139A ARG* 3.0 54.1 + - + +
143A GLU* 5.7 1.3 - - - +
139B ARG 2.9 16.2 + - - +
140B SER* 3.7 4.3 - - - +
142B GLN* 1.3 76.4 - - - +
144B LEU* 1.3 66.6 + - - +
145B LEU 3.0 1.8 - - - -
146B GLN* 2.9 17.4 + - - +
147B LEU* 3.1 43.0 + - + +
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Residues in contact with LEU 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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136A MET* 3.7 17.6 - - + +
114B ILE* 3.6 45.1 - - + +
116B PHE* 3.6 43.0 - - + +
117B ARG* 5.6 0.2 + - - -
119B VAL* 3.8 35.9 - - + +
121B VAL* 4.0 10.8 - - + -
140B SER 2.9 17.0 + - - +
141B LYS* 3.8 4.9 - - - +
143B GLU* 1.3 76.5 - - - +
145B LEU* 1.3 59.5 + - + +
146B GLN 3.6 0.3 + - - -
147B LEU* 3.9 12.9 + - + +
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PHE* 3.9 29.4 - - + -
76B TYR* 2.8 45.4 + - + -
78B ARG* 3.5 11.4 + - - -
83B LEU* 3.9 14.6 - - + -
86B VAL* 3.8 28.9 - - + -
87B LEU* 4.6 1.1 - - + -
114B ILE* 4.5 6.3 - - + -
116B PHE* 3.9 26.0 - - + -
141B LYS* 3.2 34.9 + - + +
142B GLN 4.1 0.9 - - - +
143B GLU 3.0 0.8 - - - -
144B LEU* 1.3 76.3 - - - +
146B GLN* 1.3 58.3 + - - +
147B LEU 3.6 0.4 - - - -
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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
------------------------------------------------------------
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