Contacts of the helix formed by residues 155 - 166 (chain B) in PDB entry 6XAV
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B ARG* 6.0 0.4 - - - -
153B SER* 3.2 9.5 + - - +
154B THR* 1.3 86.2 + - + +
156B ASP* 1.3 61.8 + - - +
157B LEU 3.2 4.0 + - - -
158B THR* 3.6 13.4 + - - -
186B MET* 5.4 9.6 - - - +
190B ASN* 3.0 31.0 + - - +
193B GLN* 6.3 1.1 - - - +
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Residues in contact with ASP 156 (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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148B GLU* 3.6 9.2 - - - +
149B ARG* 3.0 38.8 + - + +
150B GLY* 3.2 22.9 + - - -
151B ASN* 4.3 2.3 + - - +
152B GLY* 4.6 4.0 + - - -
153B SER* 3.3 24.3 + - - +
154B THR 3.2 1.6 - - - -
155B GLU* 1.3 75.7 - - - +
157B LEU* 1.3 57.5 + - - +
158B THR 3.2 0.4 - - - -
159B ALA* 3.1 16.2 + - - +
160B ARG* 2.9 36.1 + - - +
190B ASN* 5.1 0.4 - - - +
407B LYS 4.9 2.4 - - - +
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B SER 4.9 4.9 - - - +
154B THR* 3.5 23.8 - - - +
155B GLU 3.2 1.0 - - - -
156B ASP* 1.3 78.1 - - - +
158B THR* 1.3 62.8 + - - +
160B ARG* 3.7 31.9 - - - +
161B VAL* 3.0 33.6 + - + +
356B PRO* 5.2 8.1 - - + -
400B ILE* 4.9 22.2 - - + +
403B LEU* 3.9 21.5 - - + +
404B ALA* 4.7 12.3 - - + +
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Residues in contact with THR 158 (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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155B GLU* 3.6 10.0 + - - -
156B ASP 3.2 0.8 - - - -
157B LEU* 1.3 79.5 - - - +
159B ALA* 1.3 61.8 + - - +
161B VAL* 3.6 2.3 + - - +
162B LEU* 3.1 25.9 + - + +
187B LEU* 5.0 18.8 - - + +
190B ASN* 3.8 29.0 + - + +
191B ILE* 6.3 1.1 - - + -
356B PRO* 4.1 34.0 - - + +
358B ILE* 4.8 6.2 - - + +
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B MET* 3.2 32.1 - - + +
148B GLU* 4.2 0.2 - - - -
149B ARG* 5.3 0.4 - - + -
155B GLU 4.4 0.2 + - - -
156B ASP* 3.1 21.7 + - - +
158B THR* 1.3 76.9 - - - +
160B ARG* 1.3 64.9 + - - +
162B LEU* 3.3 7.7 + - - +
163B ASP* 3.0 31.1 + - - +
190B ASN* 3.7 15.0 + - - +
194B SER* 4.2 5.6 - - - +
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Residues in contact with ARG 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLU* 4.3 9.2 - - + -
156B ASP* 2.9 36.6 + - - +
157B LEU* 3.7 21.2 - - - +
159B ALA* 1.3 76.6 - - - +
161B VAL* 1.3 62.0 + - - +
163B ASP* 3.4 6.3 + - - +
164B LEU* 3.2 28.0 + - - +
403B LEU* 2.9 56.2 + - + +
406B THR* 3.1 15.6 + - - +
407B LYS* 3.0 26.5 + - - +
408B THR 3.2 20.0 + - - -
409B ASN* 2.4 41.5 + - - +
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 3.0 20.0 + - + +
158B THR 4.0 3.4 - - - +
160B ARG* 1.3 74.4 - - - +
162B LEU* 1.3 57.4 + - - +
164B LEU* 3.3 5.9 + - - +
165B ALA* 2.9 27.5 + - - +
356B PRO* 4.7 11.0 - - + -
358B ILE* 4.0 26.0 - - + -
360B TYR* 4.6 9.8 - - + -
396B MET* 4.6 11.9 - - + -
399B LEU* 3.7 35.0 - - + -
400B ILE* 5.8 4.7 - - + -
403B LEU* 3.8 13.9 - - + -
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Residues in contact with LEU 162 (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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147B MET* 3.8 29.6 - - + -
158B THR* 3.1 22.4 + - + +
159B ALA* 3.6 6.7 - - - +
160B ARG 3.3 0.2 - - - -
161B VAL* 1.3 78.7 - - - +
163B ASP* 1.3 59.0 + - - +
165B ALA* 4.5 4.3 - - - +
166B SER* 2.8 53.9 + - - +
168B ILE* 3.9 14.4 - - + -
187B LEU* 5.4 4.3 - - + -
190B ASN* 6.1 0.7 - - - +
191B ILE* 3.8 34.5 - - + -
343B LEU* 4.1 20.4 - - + -
358B ILE* 4.9 7.6 - - + +
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Residues in contact with ASP 163 (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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144B ARG* 3.9 20.5 + - - +
145B LEU 5.2 0.2 - - - +
146B ARG* 4.3 4.9 + - - +
147B MET* 3.3 32.3 + - - +
148B GLU* 3.1 32.7 + - - +
159B ALA 3.0 16.9 + - - +
160B ARG* 3.8 6.1 - - - +
161B VAL 3.3 0.4 - - - -
162B LEU* 1.3 80.4 - - - +
164B LEU* 1.3 62.7 + - + +
165B ALA 3.5 0.3 + - - -
166B SER 4.7 1.8 - - - -
167B PRO* 3.3 27.7 - - - +
168B ILE 5.5 0.3 + - - -
380B MET* 3.7 7.4 - - + +
409B ASN* 5.0 5.1 + - - +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ARG 3.2 15.5 + - - +
161B VAL* 3.3 5.4 + - - +
163B ASP* 1.3 77.9 - - + +
165B ALA* 1.3 59.6 + - - +
167B PRO* 5.2 0.4 - - - +
360B TYR* 2.9 30.7 + - + +
380B MET* 4.0 28.2 - - + +
383B LEU* 3.9 19.3 - - + -
384B ARG* 4.0 5.2 + - - -
399B LEU* 4.7 6.5 - - + -
403B LEU* 4.6 20.6 - - + -
409B ASN* 3.4 27.4 - - + +
412B PHE* 4.8 1.6 - - + -
413B PHE* 3.6 32.8 - - + -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B VAL* 2.9 20.0 + - + +
162B LEU* 4.1 2.0 - - - +
164B LEU* 1.3 78.5 - - - +
166B SER* 1.3 62.6 + - - +
167B PRO* 4.1 3.5 - - - +
343B LEU* 4.4 11.9 - - + -
358B ILE* 5.0 2.9 - - + -
360B TYR* 3.6 24.2 - - + -
363B SER* 4.1 15.7 - - - +
364B GLY* 3.5 9.2 - - - -
365B THR 4.5 0.2 + - - -
368B GLU* 5.4 1.2 - - - +
384B ARG* 2.7 23.1 + - - +
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 2.8 27.4 + - - +
165B ALA* 1.3 77.0 - - - +
167B PRO* 1.3 69.7 - - - +
168B ILE* 3.5 12.3 + - - +
341B MET* 4.0 20.7 - - - +
342B GLU 5.6 0.4 - - - -
343B LEU* 3.9 26.6 - - - +
364B GLY 4.2 7.2 - - - -
365B THR* 3.2 17.5 - - - -
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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