Contacts of the helix formed by residues 140 - 145 (chain A) in PDB entry 4UTX
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 GLU 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASN 5.2 0.6 + - - -
138A ILE 3.3 4.0 - - - -
139A ASP* 1.3 79.8 + - - +
141A LEU* 1.3 62.4 + - - +
142A HIS 3.2 2.7 - - - -
143A HIS* 3.0 36.1 + - + +
144A ARG* 3.1 20.8 + - + +
152A GLU* 3.8 18.2 + - - +
156A SER* 2.8 28.8 + - - +
158A PHE* 3.6 19.7 - - + +
159A LYS* 4.3 8.7 - - - -
172A HIS* 2.7 34.2 + - - -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A SER* 4.4 2.2 - - - +
61A SER* 3.9 18.4 - - - -
63A VAL* 4.1 13.0 - - + -
105A MET* 3.8 18.6 - - + -
108A LYS* 4.0 1.3 - - + +
109A MET 4.0 3.1 - - - -
110A PRO* 3.7 32.9 - - + +
114A HIS* 3.5 35.3 - - + +
139A ASP* 2.9 33.5 + - - +
140A GLU* 1.3 77.3 - - - +
142A HIS* 1.3 63.7 + - - +
144A ARG* 3.3 15.7 + - - +
145A ALA* 3.0 23.2 + - - +
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Residues in contact with HIS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A THR* 3.1 42.3 + - + +
57A VAL* 4.6 5.9 - - + +
114A HIS* 3.6 30.3 + + - -
117A ILE* 4.1 19.8 - - + +
133A ILE* 4.0 12.5 - - + +
135A THR* 3.8 21.1 - - + -
137A ASN* 5.0 4.0 + - + -
139A ASP* 5.9 1.3 - - - -
140A GLU 3.2 1.0 - - - -
141A LEU* 1.3 78.1 - - - +
143A HIS* 1.3 70.7 + - + +
145A ALA* 3.3 9.2 + - - +
146A GLY 3.3 0.2 + - - -
147A SER* 2.8 43.7 + - - -
150A VAL* 4.2 7.2 - - + -
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Residues in contact with HIS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR* 5.6 0.6 - - - +
140A GLU* 3.0 34.7 + - + +
142A HIS* 1.3 83.0 - - + +
144A ARG* 1.3 63.3 - - + +
146A GLY* 2.8 21.1 + - - -
147A SER 3.8 13.1 + - - +
148A LYS* 5.4 3.0 + - - -
150A VAL* 3.6 33.4 - - + +
152A GLU* 3.3 32.7 + - + -
1301B DMS 4.8 1.7 + - - -
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A MET* 3.2 42.0 + - - +
106A ARG* 4.9 2.6 + - - +
108A LYS 3.0 21.9 + - - -
109A MET* 3.3 21.2 - - - +
110A PRO* 4.0 12.0 - - + +
139A ASP 4.8 2.4 + - - -
140A GLU* 3.1 20.4 + - + +
141A LEU* 3.7 16.7 - - - +
143A HIS* 1.3 79.1 - - + +
145A ALA* 1.3 57.6 + - - +
158A PHE* 6.0 2.1 - - - -
115B LEU* 4.3 3.1 - - - +
119B GLU* 2.9 44.6 + - - +
1301B DMS 3.9 16.4 + - - +
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PRO* 4.1 9.0 - - + -
114A HIS* 3.6 40.2 - - + +
115A LEU* 3.9 19.8 - - + +
118A ALA* 3.2 13.4 - - + +
119A GLU* 5.7 0.9 - - - +
141A LEU 3.0 15.7 + - - +
142A HIS 3.6 6.1 - - - +
143A HIS 3.1 0.2 - - - -
144A ARG* 1.3 77.4 - - - +
146A GLY* 1.3 57.8 + - - +
147A SER 3.7 0.2 - - - -
115B LEU* 5.5 0.2 - - - -
1301B DMS 3.9 11.2 - - - +
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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