Contacts of the helix formed by residues 155 - 166 (chain A) in PDB entry 1XPU
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 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A SER* 3.6 7.9 + - - +
154A THR* 1.3 79.1 + - - +
156A ASP* 1.3 56.9 + - - +
157A LEU 2.9 11.3 + - - -
158A THR 3.8 1.4 + - - -
159A ALA* 4.9 0.3 - - - +
186A MET* 4.3 20.2 - - - +
190A ASN* 3.0 45.3 + - - +
193A GLN* 3.4 25.4 - - - +
1600A AGS 5.7 0.7 + - - -
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Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A MET 3.5 26.6 - - - +
152A GLY* 4.1 15.3 + - - -
153A SER* 3.8 25.8 + - - +
154A THR 3.3 1.0 - - - -
155A GLU* 1.3 75.5 - - - +
157A LEU* 1.3 57.1 + - - +
158A THR 3.6 0.4 - - - -
159A ALA* 3.8 14.6 - - - +
160A ARG* 3.2 37.2 + - - +
194A SER* 5.8 0.7 - - - -
197A TYR* 5.6 6.8 - - - -
407A LYS* 5.9 1.6 - - - -
408A THR* 5.1 3.2 + - - -
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Residues in contact with LEU 157 (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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153A SER 4.7 2.2 - - - +
154A THR* 3.2 35.9 + - + +
155A GLU 2.9 1.8 - - - -
156A ASP* 1.3 75.1 - - - +
158A THR* 1.3 68.1 + - - +
160A ARG* 3.3 23.5 + - - +
161A VAL* 3.3 28.5 + - + +
355A PHE* 5.0 18.2 - - + -
356A PRO* 4.8 8.3 - - + -
400A ILE* 4.5 32.3 - - + +
403A LEU* 5.3 3.8 - - + +
404A ALA* 4.7 11.0 - - + +
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Residues in contact with THR 158 (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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155A GLU 3.8 1.8 + - - -
157A LEU* 1.3 77.2 - - - +
159A ALA* 1.3 53.6 + - - +
160A ARG 3.1 0.5 + - - -
161A VAL* 3.2 4.2 + - - +
162A LEU* 2.7 39.4 + - + +
187A LEU* 3.6 32.3 - - + -
190A ASN* 3.5 27.6 - - + +
191A ILE* 6.0 0.2 - - + -
356A PRO* 3.4 39.9 - - + +
358A ILE* 4.6 2.0 - - + +
1600A AGS 3.7 14.8 + - - +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A MET* 3.8 17.4 - - + +
155A GLU 4.9 0.2 - - - +
156A ASP* 3.8 23.6 + - - +
157A LEU 3.4 0.2 - - - -
158A THR* 1.3 78.7 - - - +
160A ARG* 1.3 56.6 + - - +
162A LEU* 3.4 11.9 - - + +
163A ASP* 3.0 33.4 + - - +
190A ASN* 3.6 18.4 + - - +
194A SER* 3.7 16.6 - - - +
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Residues in contact with ARG 160 (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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147A MET 5.5 0.7 - - - -
153A SER 3.8 19.6 + - - +
156A ASP* 3.2 33.8 + - - +
157A LEU* 3.3 15.6 + - - +
158A THR 3.1 0.4 - - - -
159A ALA* 1.3 75.6 - - - +
161A VAL* 1.3 65.7 + - - +
162A LEU 3.1 1.1 - - - -
163A ASP* 3.3 6.4 + - - +
164A LEU* 3.2 26.5 + - + +
403A LEU* 2.7 66.6 + - + +
404A ALA* 3.9 4.0 - - - +
406A THR 4.0 2.8 + - - -
407A LYS* 2.8 45.3 + - - +
408A THR* 3.3 28.0 + - + +
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Residues in contact with VAL 161 (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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157A LEU* 3.4 16.6 - - + +
158A THR 3.2 5.7 + - - +
160A ARG* 1.3 75.3 - - - +
162A LEU* 1.3 57.2 + - - +
164A LEU* 3.8 8.5 - - - +
165A ALA* 2.9 27.8 + - - +
356A PRO* 4.6 8.1 - - + -
358A ILE* 4.3 19.1 - - + -
360A TYR* 4.5 8.7 - - + -
396A MET* 3.6 35.4 - - + -
399A LEU* 4.2 16.2 - - + +
400A ILE* 5.5 2.7 - - + +
403A LEU* 3.8 20.2 - - + -
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Residues in contact with LEU 162 (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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147A MET* 3.6 33.4 - - + -
158A THR* 2.7 16.3 + - + +
159A ALA* 3.4 11.0 - - - +
160A ARG 3.1 0.2 - - - -
161A VAL* 1.3 79.2 - - - +
163A ASP* 1.3 56.8 + - - +
165A ALA* 4.8 1.8 - - - -
166A SER* 2.9 38.6 + - - +
168A ILE* 4.9 11.4 - - + -
176A ILE* 5.9 0.9 - - + -
187A LEU* 3.7 27.4 - - + -
190A ASN* 5.6 0.7 - - - +
191A ILE* 3.8 22.0 - - + -
343A LEU* 3.6 26.5 - - + -
358A ILE* 4.3 7.8 - - + +
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Residues in contact with ASP 163 (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 ARG* 2.4 44.1 + - - +
145A LEU 3.5 17.3 - - - +
146A ARG* 3.4 9.5 - - + +
147A MET* 2.6 44.6 + - - +
159A ALA 3.0 14.5 + - - +
160A ARG* 3.3 4.9 + - - +
162A LEU* 1.3 76.3 - - - +
164A LEU* 1.3 58.9 + - + +
166A SER 4.8 0.2 - - - -
167A PRO* 3.4 18.9 - - - +
168A ILE* 4.6 2.7 + - - +
380A MET* 4.1 2.6 - - - +
408A THR* 5.9 5.6 - - + -
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Residues in contact with LEU 164 (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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160A ARG* 3.2 18.7 + - + +
161A VAL* 3.8 5.6 - - - +
162A LEU 3.2 0.8 - - - -
163A ASP* 1.3 80.2 - - + +
165A ALA* 1.3 63.3 + - - +
167A PRO* 4.1 1.3 - - - +
360A TYR* 3.5 23.0 + - + +
376A GLU* 5.8 1.8 - - - +
379A LYS* 4.1 21.1 - - - +
380A MET* 3.6 38.4 - - + +
383A LEU* 4.8 12.8 - - + -
384A ARG* 3.6 6.9 + - - -
399A LEU* 4.5 12.1 - - + -
403A LEU* 4.1 34.3 - - + -
408A THR* 5.2 11.2 - - + +
411A ASP* 5.6 0.2 - - - +
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A VAL 2.9 18.4 + - - +
162A LEU* 4.2 2.2 - - - +
164A LEU* 1.3 77.4 - - - +
166A SER* 1.3 60.7 + - - +
167A PRO* 3.7 1.4 - - - +
343A LEU* 4.9 1.1 - - + -
358A ILE* 4.3 10.3 - - + -
360A TYR* 3.7 26.2 - - + +
363A SER* 3.8 20.8 - - - +
364A GLY* 3.4 12.3 + - - -
384A ARG* 2.6 26.0 + - - +
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Residues in contact with SER 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 2.9 19.9 + - - +
165A ALA* 1.3 75.6 - - - +
167A PRO* 1.3 68.1 - - - +
168A ILE* 3.2 17.5 + - - +
341A MET* 3.9 26.9 - - - +
342A GLU 4.0 15.3 - - - -
343A LEU* 3.3 25.9 - - - +
363A SER* 4.9 0.2 - - - -
364A GLY 4.0 4.7 - - - -
365A THR* 4.3 4.0 - - - -
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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