Contacts of the helix formed by residues 132 - 143 (chain B) in PDB entry 4X5O
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 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B ASP* 3.1 16.0 + - - -
131B LEU* 1.3 77.6 - - - +
133B VAL* 1.3 60.0 + - - +
134B PRO 3.3 1.1 - - - -
135B PHE* 3.1 11.8 + - + +
136B ALA* 2.9 26.9 + - - +
175B ASP* 3.5 20.1 + - - +
177B ASP* 4.8 4.4 + - - +
363B TYR* 3.1 40.0 + - + +
366B LEU* 3.6 19.1 - - + -
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B THR* 4.1 15.0 - - + +
103B LEU* 3.7 25.1 - - + -
104B MET 6.0 0.9 - - - +
129B TYR* 3.3 26.2 - - + +
130B ASP* 3.5 18.0 + - + +
132B THR* 1.3 78.2 - - - +
134B PRO* 1.4 68.0 - - + +
136B ALA* 3.2 8.6 + - - +
137B ARG* 3.0 19.6 + - - +
330B TYR* 4.9 7.9 - - + -
366B LEU* 4.4 15.9 - - + -
369B MET* 5.4 2.5 - - - -
370B PHE* 3.7 14.8 - - + -
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Residues in contact with PRO 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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94B THR* 3.9 25.5 - - + +
98B GLU* 3.5 35.0 - - + +
103B LEU* 5.2 2.0 - - + -
128B ARG* 4.4 8.1 - - + -
130B ASP* 3.4 26.9 - - + +
131B LEU* 3.5 11.4 - - + +
133B VAL* 1.4 91.9 - - + +
135B PHE* 1.3 58.2 + - - +
137B ARG* 3.4 12.4 + - + +
138B TYR* 2.9 29.8 + - - +
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Residues in contact with PHE 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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92B ILE* 5.3 1.1 - - - -
131B LEU 3.4 7.2 + - - +
132B THR* 3.1 15.6 + - + +
134B PRO* 1.3 77.4 - - - +
136B ALA* 1.3 61.6 + - - +
138B TYR* 3.2 11.3 + + - +
139B LEU* 3.0 53.3 + - + +
147B ILE* 3.6 24.7 - - + -
149B ARG* 3.1 54.7 - - - +
177B ASP* 3.6 25.4 - - + -
179B ALA* 4.2 5.2 - - + -
363B TYR* 3.8 16.2 - + - -
367B VAL* 5.7 2.7 - - + -
379B CYS* 3.9 14.4 - - - -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B THR 2.9 11.2 + - - +
133B VAL* 3.3 11.2 - - - +
135B PHE* 1.3 77.6 - - - +
137B ARG* 1.3 61.8 + - - +
139B LEU 3.3 1.4 + - - -
140B ALA* 3.1 24.1 + - - +
366B LEU* 3.0 28.0 - - + +
367B VAL* 3.8 18.0 - - - +
369B MET* 3.8 7.6 - - + -
370B PHE* 3.6 16.0 - - + -
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Residues in contact with ARG 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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56A LEU* 4.6 20.0 - - + +
57A LYS 4.3 17.7 - - - +
58A THR* 3.6 9.7 - - - +
64A ASP* 2.7 43.2 + - - -
94B THR* 4.3 6.1 - - - +
95B PRO* 4.6 0.2 - - - +
98B GLU* 2.8 34.3 + - - -
102B THR* 4.2 17.5 - - + -
133B VAL 3.0 12.9 + - - +
134B PRO* 3.8 16.5 + - + +
136B ALA* 1.3 76.6 - - - +
138B TYR* 1.3 68.0 + - - +
140B ALA* 3.6 2.3 + - - +
141B MET* 3.1 51.2 + - - +
370B PHE* 3.4 18.3 - - + -
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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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64A ASP* 3.6 33.7 - - + -
65A TYR 5.1 3.1 - - - -
66A SER* 4.0 9.7 - - - -
67A PRO* 3.5 22.7 - - + +
92B ILE* 3.9 37.9 - - + -
134B PRO 2.9 17.7 + - - +
135B PHE* 3.4 9.2 - + - +
136B ALA 3.2 0.2 - - - -
137B ARG* 1.3 86.8 - - - +
139B LEU* 1.3 73.8 + - + +
141B MET* 3.3 2.0 + - + +
142B ASN* 3.1 53.5 + - - +
144B LEU* 3.9 20.0 - - + +
147B ILE* 4.4 8.7 - - + +
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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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135B PHE* 3.0 51.3 + - + +
136B ALA 3.3 0.2 + - - -
138B TYR* 1.3 77.0 - - + +
140B ALA* 1.3 61.3 + - - +
143B LYS* 2.9 9.9 + - - +
144B LEU* 2.9 67.1 + - + +
145B THR 6.1 0.9 - - - -
146B ASN 6.0 0.2 - - - +
147B ILE* 3.7 15.0 - - + -
179B ALA* 4.1 15.7 - - + -
367B VAL* 3.5 36.6 - - + -
377B VAL* 4.9 3.8 - - + -
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Residues in contact with ALA 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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56A LEU* 3.7 12.3 - - + +
136B ALA 3.1 16.1 + - - +
137B ARG 4.0 0.7 - - - +
139B LEU* 1.3 77.3 - - - +
141B MET* 1.3 62.2 + - - +
143B LYS* 3.6 14.9 + - - +
367B VAL* 4.7 7.3 - - - +
370B PHE* 3.7 26.9 - - + -
371B ASP* 3.9 21.7 - - + +
372B PRO* 5.6 3.9 - - + +
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Residues in contact with MET 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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56A LEU* 3.4 36.3 - - + +
57A LYS* 3.6 17.7 - - + -
58A THR* 4.1 11.0 - - + +
64A ASP* 4.6 2.9 - - - +
137B ARG* 3.1 43.2 + - - +
138B TYR* 3.7 3.8 - - - +
139B LEU 3.2 0.4 - - - -
140B ALA* 1.3 76.6 - - - +
142B ASN* 1.3 65.7 + - - +
143B LYS* 3.1 6.2 + - - +
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Residues in contact with ASN 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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64A ASP* 5.3 0.3 - - - +
138B TYR* 3.1 45.3 + - - +
141B MET* 1.3 82.5 - - - +
143B LYS* 1.3 71.8 + - - +
144B LEU* 3.7 25.8 - - + +
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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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139B LEU 2.9 10.7 + - - +
140B ALA* 3.6 11.6 + - - +
141B MET 3.1 5.1 - - - +
142B ASN* 1.3 82.9 - - - +
144B LEU* 1.3 62.2 + - - +
145B THR* 4.4 16.2 + - + +
371B ASP* 2.7 35.3 + - - +
373B LYS* 4.6 15.4 - - - +
375B ARG* 4.6 14.5 - - - +
377B VAL* 5.8 3.0 - - - +
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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
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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