Contacts of the helix formed by residues 121 - 129 (chain B) 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 ARG 121 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B SER 3.2 2.9 + - - -
119B PHE 2.9 1.6 + - - -
120B THR* 1.3 88.8 + - - +
122B LEU* 1.3 65.7 + - - +
123B PRO* 3.0 8.1 - - - -
124B ASP* 3.1 32.6 + - - +
125B ALA 3.7 0.2 + - - -
132B THR* 3.3 27.1 + - + +
135B SER* 3.8 43.3 + - - -
136B ILE* 3.6 22.5 - - + +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A MET* 4.7 4.5 - - + +
30A VAL* 5.1 5.4 - - + -
33A THR* 3.4 17.7 - - + -
67A LEU* 3.3 34.3 - - + -
119B PHE* 3.0 35.0 + - + +
121B ARG* 1.3 77.4 - - - +
123B PRO* 1.3 68.4 - - + +
125B ALA* 3.0 16.4 + - + -
126B ILE* 3.0 19.5 + - + -
301B LEU* 5.0 5.8 - - + -
304B LEU* 4.3 13.2 - - + -
305B VAL* 3.6 28.3 - - + -
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Residues in contact with PRO 123 (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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29A MET* 5.1 0.2 - - + -
33A THR* 3.7 28.2 - - + -
36A THR* 5.1 6.5 - - + -
37A LEU* 5.3 6.2 - - + +
108A LEU* 3.7 24.5 - - + -
120B THR 4.7 0.7 - - - +
121B ARG* 3.0 9.9 - - - -
122B LEU* 1.3 93.4 - - + +
124B ASP* 1.3 57.6 + - - +
126B ILE* 3.2 7.0 + - + +
127B ARG* 2.9 57.9 + - - +
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Residues in contact with ASP 124 (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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121B ARG* 3.1 33.6 + - - +
123B PRO* 1.3 77.5 - - - +
125B ALA* 1.3 57.9 + - - +
127B ARG* 3.3 19.4 + - - +
128B THR* 2.9 42.5 + - + +
130B ARG 4.8 0.7 - - - +
132B THR* 4.5 5.7 + - - +
135B SER* 5.4 1.6 + - - -
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Residues in contact with ALA 125 (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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63A ALA* 4.0 3.6 - - - +
121B ARG 3.7 1.4 + - - -
122B LEU* 3.0 9.5 + - + +
124B ASP* 1.3 79.7 - - - +
126B ILE* 1.3 59.6 + - - +
128B THR* 4.1 0.2 - - - -
129B GLY* 2.8 30.7 + - - -
130B ARG 3.5 22.7 - - - +
132B THR* 4.2 5.1 + - - +
304B LEU* 4.0 18.9 - - + +
305B VAL* 3.9 26.7 - - + -
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Residues in contact with ILE 126 (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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33A THR* 4.6 2.7 - - - +
37A LEU* 4.3 9.4 - - + -
59A THR* 3.5 24.4 - - + -
60A ARG* 3.2 18.5 + - - +
63A ALA* 3.3 30.4 - - - +
64A LEU* 4.1 22.9 - - + -
67A LEU* 3.8 19.7 - - + +
122B LEU* 3.0 34.6 + - + +
123B PRO* 3.2 8.3 + - + +
125B ALA* 1.3 78.0 - - - +
127B ARG* 1.3 60.4 + - - +
301B LEU* 5.2 1.1 - - + -
304B LEU* 4.1 17.7 - - + -
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Residues in contact with ARG 127 (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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36A THR* 4.2 15.8 + - - +
37A LEU* 4.0 21.3 - - + +
57A THR 4.6 4.9 + - - -
58A ASP* 4.0 28.5 - - - +
59A THR* 4.2 6.2 - - + +
60A ARG* 3.3 26.8 + - - +
123B PRO* 2.9 44.2 + - - +
124B ASP* 3.3 26.4 + - - +
126B ILE* 1.3 77.3 - - - +
128B THR* 1.3 63.9 + - + +
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Residues in contact with THR 128 (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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60A ARG* 3.3 31.7 + - - +
124B ASP* 2.9 28.2 + - + +
127B ARG* 1.3 85.3 - - + +
129B GLY* 1.3 61.2 + - - +
130B ARG* 3.0 39.7 + - - +
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Residues in contact with GLY 129 (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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60A ARG* 4.0 11.0 - - - +
63A ALA* 4.6 6.7 - - - -
66A ARG* 5.3 0.7 + - - -
125B ALA 2.8 16.0 + - - -
127B ARG 3.8 0.8 - - - -
128B THR* 1.3 76.1 - - - +
130B ARG* 1.3 60.7 + - - +
131B PRO 4.4 0.2 - - - -
304B LEU* 3.8 18.6 - - - +
308B GLY* 4.5 10.6 - - - +
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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