Contacts of the helix formed by residues 129 - 137 (chain B) in PDB entry 6TXC
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 HIS 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B MET* 4.1 15.0 - - - -
127B GLU 4.0 1.8 + - - -
128B LEU* 1.3 72.2 - - - +
130B PRO* 1.3 73.2 - - + +
131B LEU* 3.1 31.5 + - + +
132B LEU* 2.7 36.8 + - + +
133B VAL 3.1 8.1 + - - -
197B LEU* 3.7 37.9 - - + +
200B GLN* 5.1 2.9 - - - +
257B TYR* 3.5 40.2 - + - +
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Residues in contact with PRO 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 3.8 35.0 - - + +
115B MET* 4.0 12.8 - - - +
128B LEU 3.6 0.4 - - - +
129B HIS* 1.3 99.0 - - + +
131B LEU* 1.3 56.1 + - - +
133B VAL* 3.2 13.4 + - + +
134B ARG* 3.0 29.3 + - - +
253B VAL* 5.8 0.4 - - - -
257B TYR* 3.4 31.2 - - + +
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Residues in contact with LEU 131 (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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129B HIS* 3.1 17.9 + - + +
130B PRO* 1.3 77.9 - - - +
132B LEU* 1.3 63.0 + - - +
134B ARG* 3.3 6.9 + - + +
135B ILE* 3.2 21.6 + - + +
197B LEU* 4.3 17.7 - - + -
201B ILE* 3.7 28.5 - - + -
250B ILE* 4.4 10.1 - - + -
253B VAL* 3.9 22.7 - - + -
254B MET* 4.0 26.5 - - + +
257B TYR* 4.0 12.9 - - + -
259B LEU* 4.1 20.4 - - + -
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Residues in contact with LEU 132 (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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128B LEU* 4.4 16.6 - - + -
129B HIS* 2.7 36.9 + - + +
131B LEU* 1.3 69.8 - - - +
133B VAL* 1.3 59.2 + - - +
135B ILE* 3.1 6.6 + - - +
136B ILE* 2.8 38.2 + - + +
172B GLY 6.3 1.3 - - - -
197B LEU* 4.3 7.2 - - + -
200B GLN* 3.8 35.7 - - + +
201B ILE* 3.4 40.6 - - + +
204B LEU* 3.9 23.8 - - + -
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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
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114B THR 5.1 2.0 - - - +
116B LYS* 3.8 46.2 - - + +
128B LEU* 3.9 26.7 - - + +
129B HIS 3.1 4.4 + - - +
130B PRO* 3.2 13.2 + - + +
132B LEU* 1.3 75.1 - - - +
134B ARG* 1.3 60.3 + - - +
136B ILE* 3.2 11.0 + - + +
137B ASP* 2.9 45.3 + - - +
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Residues in contact with ARG 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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130B PRO 3.0 13.3 + - - +
131B LEU* 3.4 13.0 - - + +
132B LEU 3.1 0.4 - - - -
133B VAL* 1.3 80.5 - - - +
135B ILE* 1.3 60.0 + - - +
137B ASP* 3.8 8.1 + - - +
138B THR* 3.3 17.5 - - - +
248B ASN* 4.1 18.0 + - - +
249B GLY 4.8 1.4 + - - -
250B ILE* 4.1 15.7 - - + +
253B VAL* 3.4 36.6 - - + +
256B GLN* 5.8 0.4 + - - -
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Residues in contact with ILE 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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131B LEU* 3.2 20.2 + - + +
132B LEU* 3.1 8.4 + - + +
134B ARG* 1.3 75.6 - - - +
136B ILE* 1.3 60.3 + - - +
138B THR* 2.8 31.2 + - - +
141B PHE* 3.7 7.8 - - + +
201B ILE* 3.8 44.0 - - + -
204B LEU* 4.8 6.1 - - + -
205B CYS* 3.8 25.1 - - - -
241B PHE* 5.2 4.0 - - + -
244B LEU* 3.9 21.0 - - + +
245B ILE* 5.4 1.6 - - + -
250B ILE* 4.3 22.4 - - + -
254B MET* 5.9 0.9 - - + -
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Residues in contact with ILE 136 (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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128B LEU* 3.8 29.4 - - + -
132B LEU 2.8 25.6 + - - +
133B VAL* 3.5 7.2 - - + +
135B ILE* 1.3 77.7 - - - +
137B ASP* 1.3 64.2 + - - +
138B THR 3.0 7.1 + - - -
141B PHE* 3.5 39.4 - - + +
142B GLN* 3.1 25.8 + - - +
165B PHE* 4.3 9.6 - - + -
169B LEU* 3.5 21.3 - - + -
204B LEU* 4.0 15.5 - - + -
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Residues in contact with ASP 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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449A GLU 3.8 12.7 - - - +
450A TYR* 3.8 30.5 - - - +
451A ARG* 3.5 37.1 + - - +
133B VAL* 2.9 34.9 + - + +
134B ARG* 4.0 5.9 - - - +
135B ILE 3.3 0.6 - - - -
136B ILE* 1.3 78.7 - - - +
138B THR* 1.3 63.9 - - - +
142B GLN* 3.8 13.9 + - - +
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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