Contacts of the helix formed by residues 130 - 140 (chain B) in PDB entry 5C58
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 GLY 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B SER* 4.0 7.0 - - - -
123B LEU 5.6 0.2 - - - -
126B GLN* 3.5 26.8 + - - -
127B GLY 3.5 9.0 + - - -
128B HIS 3.1 3.1 - - - +
129B ASP* 1.3 81.1 - - - +
131B VAL* 1.3 65.1 + - - -
132B VAL 3.4 2.2 - - - -
133B HIS* 3.6 4.9 + - - +
134B GLN* 3.3 24.7 + - - +
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 4.4 25.1 - - + -
121B SER 3.9 14.8 - - - +
122B SER* 3.2 15.3 + - - +
126B GLN* 4.4 2.3 + - - +
129B ASP 3.8 1.8 + - - -
130B GLY* 1.3 69.9 - - - -
132B VAL* 1.3 70.3 + - + +
134B GLN* 3.6 4.1 + - - +
135B VAL* 3.1 44.1 + - + +
150B ALA* 4.5 10.3 - - + -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.0 24.2 - - + -
85B LEU* 3.3 26.0 - - + +
86B TYR* 5.0 1.3 - - - -
87B GLY 4.0 11.9 - - - +
89B LEU* 3.7 30.7 - - + +
120B LEU* 4.4 5.8 - - + +
122B SER* 3.0 28.4 + - - +
131B VAL* 1.3 82.5 - - + +
133B HIS* 1.3 61.7 + - - +
135B VAL* 4.0 3.4 - - - +
136B VAL* 3.2 30.2 + - + +
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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
----------------------------------------------------------
83B HIS 2.9 23.0 + - - -
84B THR* 3.7 3.1 - - + -
85B LEU* 3.3 40.8 + - - +
122B SER* 4.7 0.4 + - - -
127B GLY 4.0 11.7 - - - +
128B HIS* 3.6 34.6 + + + +
130B GLY* 3.6 11.5 + - - +
131B VAL 3.3 0.6 - - - -
132B VAL* 1.3 80.3 - - - +
134B GLN* 1.3 62.1 + - + +
137B TYR* 2.9 38.8 + + + +
200B HEM 3.4 48.0 - - + +
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Residues in contact with GLN 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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128B HIS* 3.2 26.4 + - - +
129B ASP* 4.0 17.4 + - - +
130B GLY 3.3 12.4 + - - +
131B VAL* 4.3 4.4 - - - +
133B HIS* 1.3 77.7 - - - +
135B VAL* 1.3 65.0 + - + +
137B TYR* 4.7 3.1 - - - -
138B GLY* 3.0 18.9 + - - -
146B ALA* 3.4 23.0 - - + +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 4.2 20.0 - - + -
92B LEU* 4.7 8.3 - - + -
120B LEU* 5.1 3.6 - - + -
131B VAL* 3.1 33.1 + - + +
132B VAL 4.0 3.6 - - - +
134B GLN* 1.3 76.8 - - - +
136B VAL* 1.3 64.2 + - + +
138B GLY* 4.1 1.0 - - - -
139B LEU* 3.2 23.2 + - + +
146B ALA* 3.7 30.6 - - + +
147B LEU* 4.1 29.7 + - + +
150B ALA* 4.4 7.2 - - + -
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Residues in contact with VAL 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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55B TYR* 4.3 17.5 - - + -
67B PHE* 4.6 7.0 - - + -
69B ALA* 4.6 18.4 - - + -
73B LEU* 5.4 0.7 - - + -
85B LEU* 3.7 30.1 - - + -
89B LEU* 5.1 5.8 - - + -
92B LEU* 6.3 0.2 - - + -
132B VAL* 3.2 25.6 + - + +
133B HIS 4.0 1.3 - - - +
135B VAL* 1.3 80.5 - - + +
137B TYR* 1.3 64.9 + - - +
138B GLY 3.1 1.8 - - - -
139B LEU* 3.0 21.1 + - + +
140B MET* 3.1 32.7 + - + +
200B HEM 4.1 1.3 - - + -
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Residues in contact with TYR 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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32B HIS* 3.6 34.2 + + + -
33B THR* 4.0 14.4 - - - +
133B HIS* 2.9 26.1 + + + +
134B GLN* 4.5 2.7 - - - +
136B VAL* 1.3 76.3 - - - +
138B GLY* 1.3 62.2 + - - +
140B MET* 3.1 14.5 + - + +
141B SER* 3.1 41.1 + - - -
200B HEM 3.4 66.4 + + + +
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Residues in contact with GLY 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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134B GLN 3.0 19.5 + - - -
135B VAL 4.1 1.3 - - - -
137B TYR* 1.3 78.7 - - - +
139B LEU* 1.3 54.7 + - - +
141B SER* 3.0 12.5 + - - -
143B ASP* 2.7 54.9 + - - -
146B ALA* 5.4 1.1 - - - -
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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
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23B TRP* 4.1 6.7 - - + -
27B PHE* 3.2 26.7 - - - -
67B PHE* 3.6 39.7 - - + -
92B LEU* 3.9 27.6 - - + -
94B PHE* 4.0 20.4 - - + -
135B VAL* 3.2 21.3 + - + +
136B VAL* 3.0 9.9 + - + +
138B GLY* 1.3 75.8 - - - +
140B MET* 1.3 58.7 + - - +
141B SER 3.2 1.5 + - - -
142B GLY 3.7 3.3 + - - +
143B ASP 4.8 0.7 - - - +
144B THR* 3.7 34.3 - - + -
147B LEU* 4.4 8.7 - - + -
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Residues in contact with MET 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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27B PHE* 4.8 0.2 - - - -
29B ASP* 3.7 1.9 - - - +
30B VAL* 3.2 37.9 + - + +
31B ASN 4.0 2.1 + - - -
32B HIS* 3.5 46.5 + - + +
41B ASN 4.7 0.2 - - - +
55B TYR* 3.4 25.8 - - - +
57B ILE* 4.3 13.0 - - + -
67B PHE* 4.3 12.3 - - + -
136B VAL* 3.1 20.4 + - - +
137B TYR* 3.4 15.3 - - + +
138B GLY 3.1 0.4 - - - -
139B LEU* 1.3 77.7 - - - +
141B SER* 1.3 59.4 + - - +
142B GLY 3.5 0.7 - - - -
200B HEM 3.7 31.9 - - + -
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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
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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