Contacts of the helix formed by residues 130 - 147 (chain B) in PDB entry 5JJA
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 ALA 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PHE 5.1 1.8 - - - +
55B PHE* 3.5 30.9 - - + +
128B GLU* 2.9 19.2 + - - +
129B ALA* 1.3 75.6 - - - +
131B TRP* 1.3 63.2 + - - +
132B PRO* 3.3 3.4 - - - -
133B HIS* 3.0 8.1 + - + +
134B LEU* 3.0 32.9 + - + +
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Residues in contact with TRP 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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128B GLU* 3.2 29.7 + - + +
130B ALA* 1.3 77.2 - - - +
132B PRO* 1.4 72.3 - - + +
134B LEU* 4.0 14.1 - - + +
135B GLN* 2.9 67.0 + - + +
138B TYR* 3.8 28.0 - + - -
175B ASP* 4.6 1.6 - - - -
177B ARG* 3.4 61.3 - - + +
178B GLU* 3.6 38.8 - - + -
181B PHE* 3.8 15.0 - + - -
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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
----------------------------------------------------------
55B PHE* 4.2 22.2 - - + -
70B ARG* 4.2 9.0 - - + +
129B ALA 3.6 10.5 - - - +
130B ALA* 3.4 3.8 - - - -
131B TRP* 1.4 93.9 - - + +
133B HIS* 1.3 64.9 + - + +
135B GLN* 4.0 13.1 - - - +
136B LEU* 3.7 21.3 - - - +
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Residues in contact with HIS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 3.6 30.2 + + - +
55B PHE* 3.6 32.7 - + + -
66B LYS* 3.1 28.4 + - - +
69B LYS* 3.6 37.2 + - + +
70B ARG* 4.2 16.2 - - + -
73B LEU* 3.8 5.8 - - + +
102B ASN* 5.3 0.2 - - - +
130B ALA* 3.0 8.4 + - + +
132B PRO* 1.3 84.4 - - + +
134B LEU* 1.3 70.2 + - + +
135B GLN 3.3 2.0 - - - -
136B LEU* 3.0 15.1 + - - +
137B VAL* 3.0 16.8 + - + +
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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
----------------------------------------------------------
102B ASN* 3.7 35.7 - - + +
103B MET* 3.9 19.9 - - + +
105B ARG* 3.7 37.0 - - - +
128B GLU* 3.8 20.4 - - + -
130B ALA* 3.0 23.7 + - + +
131B TRP* 4.0 15.3 - - + -
133B HIS* 1.3 79.8 - - + +
135B GLN* 1.3 62.4 + - - +
137B VAL* 3.2 3.9 + - + +
138B TYR* 2.9 29.6 + - - -
178B GLU* 5.2 0.7 - - - +
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TRP* 2.9 67.8 + - + +
132B PRO* 4.0 12.3 - - - +
134B LEU* 1.3 76.8 - - - +
136B LEU* 1.3 74.1 + - + +
138B TYR* 3.6 3.9 + - - +
139B GLU* 2.9 31.1 + - - +
181B PHE* 4.1 10.2 - - + -
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Residues in contact with LEU 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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70B ARG* 3.6 46.7 - - + +
73B LEU* 3.8 22.1 - - + +
74B SER* 4.2 20.0 - - - +
77B VAL* 4.3 6.6 - - + +
132B PRO 3.7 13.0 - - - +
133B HIS 3.0 7.6 + - - +
135B GLN* 1.3 86.5 - - + +
137B VAL* 1.3 60.6 + - - +
139B GLU* 3.8 24.7 - - - +
140B PHE* 2.8 31.5 + - - +
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Residues in contact with VAL 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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69B LYS* 5.4 0.2 - - - -
73B LEU* 4.1 16.8 - - + -
98B MET* 4.1 24.2 - - + -
99B PHE* 3.9 20.0 - - + -
102B ASN* 3.8 27.6 - - + +
103B MET* 3.3 22.4 - - + -
133B HIS* 3.0 16.6 + - + +
134B LEU* 3.2 8.5 + - - +
136B LEU* 1.3 73.2 - - - +
138B TYR* 1.3 64.8 + - - +
140B PHE* 3.8 5.1 - - - +
141B PHE* 3.0 24.6 + - - +
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Residues in contact with TYR 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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99B PHE* 3.8 30.3 - + - -
103B MET* 3.3 27.6 - - + +
131B TRP* 3.8 21.8 - + - -
134B LEU 2.9 23.0 + - - +
135B GLN 3.7 3.6 - - - +
137B VAL* 1.3 77.3 - - - +
139B GLU* 1.3 61.0 + - - +
141B PHE* 3.9 1.0 - - - +
142B LEU* 3.0 25.8 + - - +
167B LEU* 5.3 0.2 - - + -
170B LEU* 3.8 1.0 - - - +
178B GLU* 2.6 39.4 + - + +
181B PHE* 3.6 33.0 - - + -
182B LEU* 3.3 31.7 - - + +
185B THR* 4.3 11.9 + - - -
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 3.6 17.4 - - + +
135B GLN* 2.9 21.8 + - - +
136B LEU* 3.8 25.5 - - - +
137B VAL 3.3 0.2 - - - -
138B TYR* 1.3 75.6 - - - +
140B PHE* 1.3 58.9 + - - +
142B LEU* 3.5 3.7 + - - +
143B ARG* 3.0 60.0 + - - +
181B PHE* 4.2 17.9 - - + -
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Residues in contact with PHE 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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42B PHE* 4.1 15.9 - + - -
46B LEU* 3.8 29.6 - - + -
73B LEU* 4.9 4.3 - - + +
76B MET* 3.5 42.2 - - + -
77B VAL* 3.9 14.3 - - + +
80B ILE* 3.5 24.0 - - + -
95B VAL* 3.8 26.5 - - + -
98B MET* 3.9 17.3 - - + -
136B LEU 2.8 18.7 + - - +
137B VAL* 3.8 5.4 - - - +
139B GLU* 1.3 74.3 - - - +
141B PHE* 1.3 64.6 + - + +
143B ARG* 3.1 4.9 + - - +
144B PHE* 2.8 29.4 + + + +
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Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL* 3.9 18.8 - - + -
96B VAL* 4.3 10.5 - - + -
99B PHE* 3.5 42.4 - + + -
137B VAL 3.0 18.4 + - - +
138B TYR 3.9 3.4 - - - +
140B PHE* 1.3 80.1 - - + +
142B LEU* 1.3 57.1 + - - +
144B PHE* 3.3 23.8 - + - +
145B LEU* 2.9 54.8 + - + +
159B ILE* 4.0 18.4 - - + -
163B PHE* 3.7 31.6 - + - -
185B THR* 4.1 17.3 - - + -
189B ILE* 4.6 2.0 - - + -
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Residues in contact with LEU 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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138B TYR 3.0 16.8 + - - +
139B GLU* 3.7 4.9 - - - +
141B PHE* 1.3 78.2 - - - +
143B ARG* 1.3 57.2 + - - +
145B LEU* 3.3 11.2 + - + +
146B GLU* 3.1 48.0 + - - +
181B PHE* 4.0 28.5 - - + -
184B THR* 3.9 24.9 - - + -
185B THR* 4.4 17.7 + - - +
188B ARG* 3.8 28.7 - - + -
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Residues in contact with ARG 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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77B VAL* 3.8 15.2 - - + +
78B GLU* 5.0 3.8 + - - -
80B ILE* 3.8 16.9 - - + +
81B THR* 2.9 55.3 + - - +
139B GLU* 3.0 53.1 + - - +
140B PHE* 3.1 5.8 + - - +
142B LEU* 1.3 73.0 - - - +
144B PHE* 1.3 64.8 + - - +
146B GLU* 3.9 18.8 + - - -
147B SER* 3.1 23.9 + - - -
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Residues in contact with PHE 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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80B ILE* 3.5 13.1 - - + +
87B ILE* 3.9 34.2 - - + +
91B ILE* 4.8 1.3 - - + -
92B TYR* 3.5 34.5 - + - -
95B VAL* 3.6 49.1 - - + -
96B VAL* 4.5 7.4 - - + -
140B PHE* 2.8 16.6 + + + +
141B PHE* 3.3 29.6 - + - +
143B ARG* 1.3 78.1 - - - +
145B LEU* 1.3 68.1 + - + +
146B GLU 3.2 1.2 + - - -
147B SER* 3.4 13.9 + - - -
150B PHE* 3.3 30.9 - + - -
159B ILE* 4.8 2.7 - - + -
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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
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141B PHE* 2.9 43.7 + - + +
142B LEU* 3.3 13.7 + - + +
144B PHE* 1.3 77.5 - - + +
146B GLU* 1.3 56.8 + - + +
147B SER 3.4 0.6 - - - +
150B PHE* 3.4 50.0 - - + +
159B ILE* 4.0 20.6 - - + -
185B THR* 4.2 10.3 - - + -
188B ARG* 4.2 22.0 - - + -
189B ILE* 4.1 17.7 - - + -
192B LYS* 3.4 16.6 + - + -
193B PHE* 4.7 6.5 - - + -
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Residues in contact with GLU 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 LEU* 3.1 38.3 + - - +
143B ARG* 3.9 21.4 + - - +
144B PHE 3.3 0.2 - - - -
145B LEU* 1.3 76.0 - - - +
147B SER* 1.3 65.6 + - - +
148B PRO* 3.6 4.3 - - - +
188B ARG* 3.0 34.7 + - - +
192B LYS* 4.4 16.9 + - - +
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 4.7 9.6 + - - -
87B ILE* 3.5 24.6 - - - +
143B ARG 3.1 13.8 + - - -
144B PHE 3.4 15.6 + - - -
145B LEU 4.4 0.2 - - - +
146B GLU* 1.3 79.1 - - - +
148B PRO* 1.4 70.0 - - - +
149B ASP* 3.2 14.4 + - - +
150B PHE* 3.0 25.9 + - - +
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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