Contacts of the helix formed by residues 118 - 134 (chain B) in PDB entry 5OIV
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 VAL 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TRP* 3.6 39.9 - - + +
45B ALA* 3.5 25.6 - - + +
46B PHE* 4.0 25.6 - - + -
49B ILE* 5.4 0.9 - - - +
116B PRO 3.0 4.5 + - - +
117B PRO* 1.3 71.0 - - - +
119B HIS* 1.3 64.7 + - + +
120B ALA 3.3 1.1 - - - -
121B ILE* 3.1 35.4 + - + +
122B ALA 3.4 4.2 + - - -
258B ILE* 3.7 25.4 - - + -
387B LEU* 4.6 6.3 - - + -
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Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B SER* 3.0 41.7 + - - -
42B TRP* 4.4 1.3 - - - -
45B ALA* 3.9 17.0 - - + -
63B LEU* 4.7 8.6 - - + +
66B LEU* 3.4 24.0 - - + +
67B LEU* 6.5 0.2 - - + -
76B ILE* 4.2 6.7 - - + -
116B PRO 3.6 20.0 - - - -
117B PRO* 3.1 4.6 - - - +
118B VAL* 1.3 77.9 - - - +
120B ALA* 1.3 65.0 + - - +
122B ALA* 3.0 7.3 + - - +
123B VAL* 3.0 25.5 + - + +
152B LEU* 4.6 15.5 - - + -
155B TRP* 3.1 36.9 + + + +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PRO 4.3 1.6 + - - -
118B VAL 3.3 1.0 - - - -
119B HIS* 1.3 78.0 - - - +
121B ILE* 1.3 57.4 + - - +
123B VAL* 3.2 11.5 + - - +
124B GLN 2.9 23.2 + - - -
152B LEU* 5.3 3.4 - - + +
156B HIS* 4.4 8.7 + - - +
262B ALA* 3.5 35.7 - - + +
265B VAL* 3.5 15.5 - - + +
266B LEU* 4.1 22.4 - - + -
269B ILE* 4.2 0.5 - - - +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PHE* 6.3 0.4 - - + -
49B ILE* 4.3 4.0 - - + -
118B VAL* 3.1 26.3 + - + +
120B ALA* 1.3 77.1 - - - +
122B ALA* 1.3 64.0 + - - +
124B GLN* 3.2 8.2 + - - +
125B ARG* 3.0 22.5 + - + +
258B ILE* 5.3 5.2 - - + -
261B VAL* 4.3 16.4 - - + -
262B ALA* 5.1 6.3 - - + +
265B VAL* 4.4 6.1 - - + -
386B TRP* 3.9 30.3 - - + -
387B LEU* 4.1 22.0 - - + -
390B TRP* 3.8 42.6 - - + +
391B CYS* 5.1 0.7 - - - -
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA* 3.3 40.2 - - + +
48B ALA* 4.3 10.3 - - + -
49B ILE* 3.5 15.7 - - + +
63B LEU* 4.3 6.1 - - + -
118B VAL 3.4 2.4 + - - -
119B HIS* 3.0 9.7 + - - +
121B ILE* 1.3 80.2 - - - +
123B VAL* 1.3 62.6 + - - +
125B ARG* 3.1 2.9 + - - +
126B ILE* 2.9 29.7 + - - +
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.9 17.9 - - + -
119B HIS* 3.0 20.3 + - + +
120B ALA* 3.2 10.3 + - - +
122B ALA* 1.3 75.2 - - - +
124B GLN* 1.3 62.7 + - - +
126B ILE* 3.3 9.3 + - + +
127B LEU* 3.0 34.7 + - + +
144B PHE* 3.9 18.8 - - + -
145B LEU* 4.1 19.3 - - + -
152B LEU* 4.2 19.3 - - + -
266B LEU* 5.3 1.8 - - + -
269B ILE* 3.8 17.7 - - + -
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Residues in contact with GLN 124 (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 ALA 2.9 13.0 + - - +
121B ILE* 3.2 10.1 + - - +
123B VAL* 1.3 75.7 - - - +
125B ARG* 1.3 62.4 + - - +
127B LEU* 3.3 5.4 + - - +
128B GLU* 2.9 53.8 + - + +
131B ARG* 5.9 1.1 - - - +
265B VAL* 3.3 34.8 - - + +
268B GLU* 4.6 7.2 + - - +
269B ILE* 3.9 12.6 - - + +
390B TRP* 3.9 21.4 - - + +
394B ARG* 5.1 4.2 + - - +
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A GLU* 4.3 2.6 + - - -
502A GOL 2.9 41.4 + - - -
49B ILE* 4.1 31.2 - - + -
52B ALA* 4.6 1.1 - - + -
121B ILE* 3.0 17.3 + - + +
122B ALA 3.1 6.0 + - - +
124B GLN* 1.3 77.0 - - + +
126B ILE* 1.3 62.3 + - - +
128B GLU* 2.8 39.9 + - - +
129B HIS* 3.0 47.0 + - + -
386B TRP* 4.7 3.8 - - + -
390B TRP* 3.8 27.5 - - + +
443B ASP* 2.9 36.1 + - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 4.2 9.6 - - + +
52B ALA* 4.1 12.6 - - + -
56B VAL* 4.0 26.3 - - + +
59B ALA* 4.0 33.0 - - + +
60B VAL* 4.1 16.2 - - + +
63B LEU* 3.6 30.7 - - + -
122B ALA 2.9 18.0 + - - +
123B VAL* 3.7 6.7 - - + +
125B ARG* 1.3 77.5 - - + +
127B LEU* 1.3 59.4 + - + +
129B HIS* 3.4 2.8 + - - +
130B ALA* 2.9 27.0 + - - +
141B ALA* 4.3 8.5 - - + -
144B PHE* 5.6 4.3 - - + -
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B VAL* 3.0 29.2 + - + +
124B GLN* 3.7 5.6 - - + +
126B ILE* 1.3 77.1 - - + +
128B GLU* 1.3 56.8 + - - +
130B ALA* 3.2 4.2 + - - +
131B ARG* 2.9 50.6 + - + +
141B ALA* 3.9 26.2 - - + +
142B GLU* 5.0 0.9 - - + +
144B PHE* 6.5 0.2 - - + -
145B LEU* 4.2 12.8 - - + -
269B ILE* 3.9 41.7 - - + -
273B TYR* 3.8 28.7 - - + +
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A GLU* 3.6 33.5 + - + +
502A GOL 3.8 6.9 - - - +
124B GLN* 2.9 48.1 + - + +
125B ARG* 2.8 46.5 + - - +
126B ILE 3.3 0.2 - - - -
127B LEU* 1.3 78.8 - - - +
129B HIS* 1.3 62.9 + - - +
131B ARG* 3.4 30.0 + - - +
132B THR* 3.4 19.2 + - - +
390B TRP* 5.1 1.0 + - - -
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Residues in contact with HIS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A GOL 3.6 34.0 - - - -
49B ILE 4.9 0.4 + - - -
52B ALA* 3.4 29.8 + - + +
53B PRO* 3.6 41.1 - - + +
56B VAL* 4.3 4.5 - - + -
125B ARG* 3.0 52.6 + - + +
126B ILE 3.7 3.6 - - - +
128B GLU* 1.3 76.5 - - - +
130B ALA* 1.3 59.6 + - - +
132B THR* 2.7 31.7 + - - -
133B ARG* 3.4 13.0 + - + +
443B ASP* 4.7 3.0 + - - -
446B GLY* 6.5 0.4 - - - -
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 4.2 4.9 - - + +
126B ILE 2.9 18.4 + - - +
127B LEU* 3.7 4.3 - - + +
129B HIS* 1.3 76.2 - - - +
131B ARG* 1.3 63.6 + - + +
133B ARG* 3.0 13.0 + - - +
134B GLY 3.7 5.0 + - - +
137B THR* 3.8 27.1 - - + +
138B ARG* 3.3 18.3 + - + +
141B ALA* 3.8 25.6 - - + -
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A GLU* 5.7 2.0 - - - +
124B GLN* 5.9 1.0 - - - +
127B LEU* 2.9 33.0 + - + +
128B GLU* 3.6 32.6 + - - +
129B HIS 3.2 0.4 - - - -
130B ALA* 1.3 76.3 - - + +
132B THR* 1.3 59.2 + - + +
133B ARG 3.3 0.2 - - - -
138B ARG* 3.0 39.4 + - + +
272B ASP* 5.0 9.2 + - - +
273B TYR* 3.0 40.0 + - - +
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Residues in contact with THR 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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399A GLU* 4.0 15.9 - - - +
402A ARG* 4.1 12.1 - - - +
403A LEU* 4.4 13.2 - - + -
502A GOL 4.4 10.9 - - - -
128B GLU 3.4 15.0 - - - +
129B HIS* 2.7 20.5 + - - -
131B ARG* 1.3 78.4 - - + +
133B ARG* 1.3 80.6 + - - +
134B GLY 3.6 0.7 - - - -
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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
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56B VAL* 5.1 4.5 - - + -
129B HIS* 3.4 16.4 - - + +
130B ALA 3.0 3.1 + - - +
132B THR* 1.3 97.7 + - - +
134B GLY* 1.3 61.4 + - - +
137B THR* 3.7 35.1 + - + +
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Residues in contact with GLY 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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130B ALA 3.7 0.4 + - - -
132B THR 3.6 1.6 + - - -
133B ARG* 1.3 80.3 - - - +
135B ARG* 1.3 65.9 + - - -
136B SER 3.5 1.6 - - - -
137B THR 3.3 3.1 + - - -
138B ARG* 3.0 47.0 + - - +
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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