Contacts of the helix formed by residues 140 - 147 (chain A) in PDB entry 1TW2
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 PRO 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A TYR* 4.6 1.1 - - + -
134A GLU* 3.6 29.6 - - + +
139A LYS* 1.3 85.4 - - + +
141A PHE* 1.3 65.8 + - - +
142A TYR 3.4 1.6 - - - +
143A GLU* 3.1 44.1 + - + +
144A ASP* 3.0 18.9 + - - +
307A LEU* 6.4 0.2 - - + -
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Residues in contact with PHE 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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111A ALA* 5.0 6.1 - - + -
112A VAL* 6.2 1.1 - - + -
115A ALA* 4.3 12.6 - - + -
133A TYR* 3.7 42.0 - + + -
139A LYS 3.8 0.2 + - - -
140A PRO* 1.3 73.0 - - - +
142A TYR* 1.3 93.4 + + - +
144A ASP* 3.4 4.9 - - - +
145A LEU* 3.3 39.0 + - + +
155A PHE* 3.5 33.9 - + - -
306A PHE* 3.7 18.1 + + + +
307A LEU* 3.7 32.5 - - + +
600A ERT 3.8 15.7 - + - -
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Residues in contact with TYR 142 (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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140A PRO* 3.4 1.0 - - - +
141A PHE* 1.3 107.9 - + - +
143A GLU* 1.3 61.6 + - - +
145A LEU* 3.6 12.4 + - + +
146A ALA* 3.1 24.3 + - - +
152A ARG* 4.3 3.2 + - - -
155A PHE* 3.9 11.0 - + - -
210A MET* 3.0 38.7 - - + +
256A ASN* 2.6 35.6 + - + -
257A TRP* 4.5 11.0 - + + -
307A LEU* 4.3 14.1 - - + +
600A ERT 3.5 10.4 - + - -
635A SAH 3.5 44.3 - + + +
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Residues in contact with GLU 143 (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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139A LYS* 4.1 21.3 - - + +
140A PRO* 3.1 38.1 + - + +
142A TYR* 1.3 77.3 - - + +
144A ASP* 1.3 65.1 + - - +
146A ALA* 3.0 21.9 + - + +
147A GLY* 3.2 4.7 + - - -
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Residues in contact with ASP 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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114A ARG* 2.8 23.1 + - - -
133A TYR* 2.5 34.8 + - + +
137A TYR* 4.2 15.2 - - - +
139A LYS* 3.9 18.7 + - + +
140A PRO 3.0 12.0 + - - +
141A PHE 3.4 10.3 - - - +
143A GLU* 1.3 74.9 - - - +
145A LEU* 1.3 64.1 + - - +
147A GLY* 3.1 13.3 + - - -
148A ARG* 3.2 19.9 + - - +
151A LEU* 4.0 7.4 - - - +
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Residues in contact with LEU 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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111A ALA* 4.6 7.4 - - + -
133A TYR* 4.8 8.7 - - - +
141A PHE* 3.3 34.1 + - + +
142A TYR* 3.9 15.0 - - + +
143A GLU 3.3 0.2 - - - -
144A ASP* 1.3 80.4 - - - +
146A ALA* 1.3 62.3 + - - +
147A GLY 3.3 0.3 + - - -
148A ARG* 3.4 18.0 + - - +
149A PRO* 4.3 0.3 - - - +
151A LEU* 3.6 33.9 - - + +
152A ARG* 3.5 37.4 - - - +
155A PHE* 3.8 37.2 - - + -
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Residues in contact with ALA 146 (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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142A TYR 3.1 13.8 + - - +
143A GLU* 3.0 17.7 + - + +
145A LEU* 1.3 77.0 - - - +
147A GLY* 1.3 56.3 - - - +
148A ARG 3.5 0.4 + - - -
149A PRO* 5.0 4.3 - - - +
152A ARG* 5.3 4.7 - - - +
210A MET* 6.5 0.9 - - - -
211A ALA 6.1 0.7 - - - -
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Residues in contact with GLY 147 (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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139A LYS* 5.5 8.8 + - - -
143A GLU 3.2 7.6 + - - -
144A ASP 3.1 7.3 + - - -
146A ALA* 1.3 77.2 - - - +
148A ARG* 1.3 67.0 + - - +
149A PRO* 3.8 7.4 - - - +
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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