Contacts of the helix formed by residues 133 - 143 (chain L) in PDB entry 4DVQ
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 ASN 133 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109L CYS* 3.3 22.2 - - - -
110L ARG* 3.0 33.2 + - - +
112L ILE* 4.4 19.0 - - - +
131L LEU 3.9 6.3 + - - -
132L LEU* 1.3 74.9 + - - +
134L GLY* 1.3 69.9 + - - +
136L GLU* 3.9 7.1 + - - +
137L TRP* 3.3 13.8 + - - -
448L ARG* 2.7 28.3 + - - +
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Residues in contact with GLY 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107L HIS* 3.5 28.8 + - - +
108L PRO 5.0 1.4 + - - -
109L CYS* 5.5 1.2 - - - -
133L ASN* 1.3 82.1 + - - +
135L PRO* 1.3 73.9 - - - +
137L TRP* 3.1 15.7 + - - +
138L ARG 3.4 3.3 + - - -
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Residues in contact with PRO 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107L HIS* 3.6 31.4 - - + +
134L GLY* 1.3 84.4 - - - +
136L GLU* 1.3 57.0 + - - +
138L ARG* 3.5 3.1 + - - +
139L PHE* 3.1 26.9 + - - +
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Residues in contact with GLU 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L LYS* 3.2 32.6 + - - -
132L LEU* 3.4 32.1 - - + +
133L ASN 4.2 5.4 - - - +
134L GLY 3.1 0.8 + - - -
135L PRO* 1.3 75.7 - - - +
137L TRP* 1.3 67.0 + - - +
139L PHE* 3.3 7.3 + - + +
140L ASN* 3.0 35.2 + - - +
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Residues in contact with TRP 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L LEU 3.5 23.1 - - - -
107L HIS* 4.5 6.7 - - - -
108L PRO* 3.9 12.6 - - + -
129L VAL* 3.4 22.7 - - + +
132L LEU* 3.8 17.3 - - + +
133L ASN* 3.3 17.6 + - - +
134L GLY 3.1 14.9 + - - +
136L GLU* 1.3 78.9 - - - +
138L ARG* 1.3 85.7 + - + +
140L ASN* 3.1 4.2 + - - +
141L ARG* 2.7 58.3 + - + +
447L MET* 3.6 35.9 - - + -
448L ARG* 3.0 41.8 - - + +
601L HEM 2.8 19.7 + - - -
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Residues in contact with ARG 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L LEU* 3.0 49.9 + - - +
107L HIS* 3.6 28.3 - - + +
134L GLY 3.4 2.0 + - - -
135L PRO 3.8 7.6 - - - +
136L GLU 3.3 0.4 - - - -
137L TRP* 1.3 99.8 - - + +
139L PHE* 1.3 66.9 + - - +
141L ARG* 4.4 1.8 - - + -
142L LEU* 3.1 59.7 + - + +
447L MET* 4.6 21.2 - - - +
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Residues in contact with PHE 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L PRO 3.1 17.6 + - - +
136L GLU* 3.3 8.5 + - + +
138L ARG* 1.3 78.3 - - - +
140L ASN* 1.3 65.8 + - - +
142L LEU* 4.3 1.2 - - - +
143L ARG* 2.9 78.0 + - - +
298L GLU 4.1 10.1 - - - -
299L LEU* 3.6 20.4 - - + -
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Residues in contact with ASN 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127L CYS 4.7 3.4 + - - -
129L VAL* 3.9 12.8 - - + -
132L LEU* 3.8 20.0 - - + +
136L GLU* 3.0 24.3 + - - +
137L TRP 3.4 7.0 - - - +
139L PHE* 1.3 79.1 - - - +
141L ARG* 1.3 65.9 + - - +
143L ARG* 2.9 14.6 + - - +
144L LEU* 3.2 18.9 + - + +
299L LEU* 4.0 16.9 - - - +
303L ALA* 4.1 15.8 - - - +
307L ASN* 2.8 33.1 + - - +
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Residues in contact with ARG 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L VAL* 3.8 10.3 - - - +
137L TRP* 2.7 46.5 + - + +
138L ARG* 3.3 3.6 + - - +
140L ASN* 1.3 73.8 - - - +
142L LEU* 1.3 66.3 + - + +
143L ARG 3.2 0.3 + - - -
144L LEU* 3.2 3.7 + - - +
145L ASN* 2.7 63.7 + - - +
149L LEU* 3.3 20.8 - - - +
447L MET* 3.3 21.2 + - + +
448L ARG 3.6 0.8 + - - -
449L GLN* 2.8 34.3 + - - +
451L LEU* 3.7 17.0 - - - +
601L HEM 2.8 45.7 + - - +
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Residues in contact with LEU 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138L ARG* 3.1 57.6 + - + +
139L PHE* 4.3 4.3 - - - +
141L ARG* 1.3 78.8 - - + +
143L ARG* 1.3 73.3 + - + +
144L LEU 3.3 0.9 - - - -
145L ASN* 4.5 12.9 - - + +
146L PRO* 3.1 24.7 - - - +
447L MET* 5.4 9.2 - - - -
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Residues in contact with ARG 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L PHE* 2.9 70.7 + - - +
140L ASN 2.9 9.5 + - - +
142L LEU* 1.3 92.5 - - + +
144L LEU* 1.3 62.2 + - - +
146L PRO* 4.2 5.6 - - - +
147L ASP* 5.2 1.0 + - - +
293L LEU* 3.6 19.2 - - - +
298L GLU* 3.8 43.9 + - + +
299L LEU* 4.0 16.6 - - + +
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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