Contacts of the helix formed by residues 133 - 150 (chain A) in PDB entry 2XT6
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 ALA 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ILE 3.4 2.0 + - - -
132A PRO* 1.3 69.6 - - - +
134A LYS* 1.3 56.2 + - - +
135A LEU 3.4 2.0 - - - -
136A MET* 3.3 11.3 + - + +
137A ILE* 2.8 38.2 + - + +
283A MET* 3.4 35.0 - - + -
304A LYS 3.1 15.0 + - - +
306A ILE* 3.6 19.5 - - + +
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PRO* 3.4 4.8 - - + -
133A ALA* 1.3 75.8 - - - +
135A LEU* 1.4 57.9 + - - +
137A ILE* 3.8 7.1 - - - +
138A ASP* 3.0 60.7 + - - +
302A ILE 5.2 2.0 - - - +
303A GLY* 4.1 18.6 - - - -
304A LYS 4.0 5.0 + - - +
355A TRP* 4.2 13.7 - - + -
412A LEU* 3.4 36.3 + - + -
413A TRP* 3.6 36.3 - - + +
416A ASP* 3.8 19.4 + - - -
433A ARG* 3.9 1.0 - - - +
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PRO 4.8 1.2 + - - -
133A ALA 3.4 0.6 - - - -
134A LYS* 1.4 78.2 - - - +
136A MET* 1.3 56.6 + - - +
138A ASP* 3.9 1.3 - - - +
139A ASN* 2.9 36.4 + - - +
333A LEU 3.9 9.9 - - - +
334A LEU* 3.6 35.2 - - + +
335A ASP 4.9 1.3 - - - +
336A ASP* 6.0 0.7 - - - +
339A PHE* 3.7 27.8 - - + -
353A VAL* 3.2 32.3 - - + +
354A ARG* 3.5 21.3 - - - +
355A TRP* 3.5 13.2 - - + +
412A LEU* 3.9 14.5 - - + +
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Residues in contact with MET 136 (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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133A ALA* 3.3 12.7 + - - +
135A LEU* 1.3 75.3 - - - +
137A ILE* 1.3 58.8 + - - +
139A ASN* 3.9 1.2 - - - +
140A ARG* 3.0 31.2 + - - +
157A PHE* 3.4 50.7 - - + +
160A LEU* 3.8 26.9 - - + +
161A LEU* 4.2 17.0 - - + +
283A MET* 4.4 4.7 - - + -
306A ILE* 3.7 26.2 - - + -
333A LEU* 4.1 30.7 + - + +
339A PHE* 4.1 11.8 - - + -
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Residues in contact with ILE 137 (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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133A ALA* 2.8 40.4 + - + +
134A LYS* 3.8 6.3 - - - +
136A MET* 1.3 70.8 - - - +
138A ASP* 1.3 70.5 + - - +
140A ARG* 3.3 4.2 + - - +
141A VAL* 3.1 36.3 + - + +
157A PHE* 3.6 30.0 - - + -
283A MET* 4.2 9.0 - - + -
304A LYS* 4.1 29.2 - - + -
433A ARG* 5.8 1.1 - - - +
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Residues in contact with ASP 138 (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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134A LYS* 3.0 44.1 + - - +
135A LEU 3.9 2.5 - - - +
137A ILE* 1.3 83.8 - - - +
139A ASN* 1.3 61.9 + - - +
141A VAL* 3.3 9.6 + - - +
142A VAL* 3.2 23.9 + - - +
353A VAL* 3.7 19.9 - - + +
412A LEU* 3.7 14.6 - - - +
415A LEU* 3.3 17.8 - - + +
433A ARG* 2.9 27.3 + - - +
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Residues in contact with ASN 139 (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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135A LEU* 2.9 27.9 + - - +
136A MET 4.2 0.2 - - - +
138A ASP* 1.3 73.4 - - - +
140A ARG* 1.4 54.1 + - - +
142A VAL* 3.1 4.2 + - - +
143A ILE* 2.8 41.2 + - + +
339A PHE* 3.6 40.3 - - + +
343A PHE* 3.3 20.7 - - + -
352A PRO* 3.5 0.8 - - - +
353A VAL* 2.8 50.0 + - - +
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Residues in contact with ARG 140 (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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136A MET 3.0 18.3 + - - +
137A ILE 3.3 6.0 + - - +
139A ASN* 1.4 73.3 - - - +
141A VAL* 1.4 53.6 + - + +
143A ILE* 3.7 8.9 - - - +
144A ASN* 2.8 56.3 + - - +
154A LYS* 4.2 19.2 - - - +
155A ILE* 2.6 51.4 + - + +
156A SER* 3.9 6.9 - - - +
157A PHE* 3.4 55.2 - - + +
160A LEU* 4.5 6.4 - - + +
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Residues in contact with VAL 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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137A ILE* 3.1 27.2 + - + +
138A ASP* 3.6 10.1 - - - +
139A ASN 3.3 0.2 - - - -
140A ARG* 1.4 72.2 - - + +
142A VAL* 1.3 61.6 + - + +
144A ASN* 3.9 3.2 - - - +
145A ASN* 2.9 55.0 + - - +
433A ARG* 4.8 24.2 - - + +
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Residues in contact with VAL 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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138A ASP 3.2 11.6 + - - +
139A ASN* 3.1 8.6 + - - +
141A VAL* 1.3 78.2 - - + +
143A ILE* 1.3 61.5 + - - +
145A ASN* 3.3 8.7 + - - +
146A HIS* 3.1 23.1 + - + +
343A PHE* 3.5 33.4 - - + -
348A ILE* 4.8 5.2 - - + -
351A GLU 5.5 1.8 - - - +
352A PRO* 5.6 0.2 - - + -
353A VAL* 3.9 20.2 - - + -
440A ARG* 3.6 29.6 + - - +
445A ARG* 5.6 0.3 + - - -
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Residues in contact with ILE 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 ASN* 2.8 31.3 + - + +
140A ARG* 3.7 8.1 - - - +
142A VAL* 1.3 71.7 - - - +
144A ASN* 1.3 58.0 + - - +
146A HIS* 3.2 5.7 + - - +
147A LEU* 3.1 34.9 + - + +
155A ILE* 3.7 23.1 - - + -
160A LEU* 4.8 11.0 - - + -
339A PHE* 5.2 1.6 - - + -
342A ILE* 3.7 22.2 - - + -
343A PHE* 3.6 28.5 - - + -
346A LEU* 3.6 22.0 - - + -
348A ILE* 3.7 18.1 - - + +
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Residues in contact with ASN 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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140A ARG* 2.8 58.0 + - - +
141A VAL* 4.4 3.3 - - - +
143A ILE* 1.3 69.1 - - - +
145A ASN* 1.3 64.4 + - - +
147A LEU* 4.0 7.9 - - - +
148A LYS* 3.1 28.5 + - - +
153A GLY 5.0 1.8 - - - +
154A LYS* 3.6 22.9 - - + +
155A ILE* 2.8 33.6 + - - +
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Residues in contact with ASN 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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141A VAL* 2.9 40.1 + - - +
142A VAL* 3.5 9.2 - - - +
143A ILE 3.3 0.2 - - - -
144A ASN* 1.3 75.2 - - - +
146A HIS* 1.4 61.9 + - - +
148A LYS* 3.4 14.7 - - - +
149A ARG* 3.4 26.0 + - - +
437A SER* 4.6 17.8 - - - -
445A ARG* 4.4 14.9 - - - +
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Residues in contact with HIS 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 VAL* 3.1 11.8 + - + +
143A ILE 3.4 9.0 - - - +
145A ASN* 1.4 73.8 - - - +
147A LEU* 1.3 64.3 + - + +
149A ARG* 3.0 5.0 + - - +
150A THR* 2.9 61.5 + - + +
346A LEU 5.0 4.0 + - - -
347A GLY 4.0 14.2 + - - -
348A ILE* 3.6 30.3 - - + -
349A PRO* 3.8 11.4 - - + -
350A TYR* 3.5 26.6 - + + -
386A ASP* 4.9 6.1 - - - -
391A ARG* 5.0 2.0 + - - -
440A ARG* 6.3 0.7 - - - +
445A ARG* 3.2 28.8 + - - +
446A HIS* 6.1 0.2 - - - -
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Residues in contact with LEU 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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143A ILE* 3.1 38.1 + - + +
144A ASN* 4.0 10.8 - - - +
146A HIS* 1.3 77.0 - - + +
148A LYS* 1.4 62.4 + - - +
150A THR* 3.0 17.5 + - - +
151A ARG* 5.7 2.5 - - + -
152A GLY* 2.8 41.5 + - - +
153A GLY* 3.3 33.0 - - - +
154A LYS 4.1 1.6 - - - +
155A ILE* 4.2 10.8 - - + -
346A LEU* 4.9 27.1 - - + +
348A ILE* 5.7 0.4 - - + -
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Residues in contact with LYS 148 (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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144A ASN 3.1 21.1 + - - +
145A ASN* 3.4 14.1 - - - +
147A LEU* 1.4 75.1 - - - +
149A ARG* 1.3 57.5 + - + +
152A GLY* 5.0 1.3 - - - -
153A GLY 4.8 1.7 + - - -
781A ARG* 3.4 28.4 + - + +
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Residues in contact with ARG 149 (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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145A ASN 3.4 12.5 + - - +
146A HIS 3.0 9.1 + - - +
148A LYS* 1.3 80.0 - - + +
150A THR* 1.4 62.0 + - + +
441A ASP* 3.8 43.1 + - - +
445A ARG* 3.8 35.6 - - - +
446A HIS* 4.6 9.9 + - + -
470A LYS* 6.3 0.8 - - - +
471A HIS* 3.8 32.3 + - - +
713A ASP* 4.9 3.1 - - - +
781A ARG* 3.6 10.9 + - - -
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Residues in contact with THR 150 (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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146A HIS* 2.9 55.0 + - + +
147A LEU* 3.0 12.9 + - - +
149A ARG* 1.4 82.8 - - + +
151A ARG* 1.3 78.1 + - - +
152A GLY 3.5 1.8 - - - -
386A ASP* 5.9 0.2 - - - +
445A ARG* 5.4 2.5 - - - +
446A HIS* 4.2 22.0 - - + +
777A ALA* 3.9 5.5 - - - +
781A ARG* 2.5 29.7 + - - +
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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