Contacts of the helix formed by residues 155 - 166 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D ARG* 5.9 3.1 - - + -
153D SER* 3.2 18.0 + - - +
154D THR* 1.3 97.2 + - - +
156D ASP* 1.3 60.6 + - - +
157D LEU 3.2 0.9 + - - -
158D THR* 3.7 10.5 + - - -
190D ASN* 2.9 31.8 + - - +
193D GLN* 5.4 7.9 - - - +
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Residues in contact with ASP 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D GLU* 3.3 11.3 - - - +
149D ARG* 2.9 48.0 + - + +
150D GLY* 3.0 14.9 + - - -
151D ASN* 4.3 6.5 + - - +
152D GLY* 4.9 2.3 + - - +
153D SER* 3.1 17.5 + - - +
155D GLU* 1.3 75.4 - - - +
157D LEU* 1.3 59.5 + - - +
158D THR 3.2 0.2 - - - -
159D ALA* 3.1 18.2 + - - +
160D ARG* 2.8 36.7 + - - +
407D LYS 5.0 1.9 - - - +
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D SER 4.8 4.3 - - - +
154D THR* 3.5 33.2 - - - +
155D GLU 3.2 1.4 - - - -
156D ASP* 1.3 76.4 - - - +
158D THR* 1.3 61.6 + - - +
160D ARG* 3.8 31.4 - - - +
161D VAL* 3.1 33.7 + - + +
356D PRO* 5.1 9.0 - - + -
400D ILE* 5.4 15.7 - - + +
403D LEU* 4.5 19.5 - - + +
404D ALA* 5.2 7.6 - - + +
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Residues in contact with THR 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D THR 5.5 0.5 + - - -
155D GLU* 3.7 6.6 + - - -
156D ASP 3.2 0.4 - - - -
157D LEU* 1.3 79.9 - - - +
159D ALA* 1.3 56.6 + - - +
161D VAL* 3.5 2.5 + - - +
162D LEU* 3.1 30.3 + - + +
187D LEU* 4.4 24.9 - - + +
190D ASN* 3.8 24.5 - - + +
191D ILE* 6.1 1.6 - - + -
356D PRO* 3.7 37.9 - - + +
358D ILE* 4.6 4.5 - - + +
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Residues in contact with ALA 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D MET* 3.3 35.9 - - + +
156D ASP* 3.1 18.8 + - - +
158D THR* 1.3 76.5 - - - +
160D ARG* 1.3 61.1 + - - +
162D LEU* 3.3 7.7 + - - +
163D ASP* 2.9 35.9 + - - +
190D ASN* 3.9 14.8 - - - +
194D SER* 4.3 4.7 - - - +
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Residues in contact with ARG 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D GLU* 4.0 19.7 - - + -
152D GLY* 5.9 0.2 - - - -
153D SER 5.9 0.4 + - - -
156D ASP* 2.8 34.0 + - - +
157D LEU* 3.8 19.8 - - - +
158D THR 3.3 0.2 - - - -
159D ALA* 1.3 77.1 - - - +
161D VAL* 1.3 61.6 + - - +
163D ASP* 3.4 6.2 + - - +
164D LEU* 3.2 29.5 + - - +
403D LEU* 3.1 58.2 + - + +
406D THR* 3.6 7.5 + - - +
407D LYS* 2.7 33.7 + - - +
408D THR 3.6 15.0 + - - -
409D ASN* 2.4 41.3 + - - +
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Residues in contact with VAL 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 3.1 19.9 + - + +
158D THR* 4.0 4.7 - - - +
160D ARG* 1.3 75.8 - - - +
162D LEU* 1.3 58.6 + - - +
164D LEU* 3.3 5.9 + - - +
165D ALA* 2.9 27.9 + - - +
356D PRO* 5.1 5.8 - - + -
358D ILE* 3.9 31.2 - - + -
360D TYR* 4.6 8.1 - - + -
396D MET* 4.7 12.1 - - + -
399D LEU* 3.7 34.3 - - + -
400D ILE* 6.0 4.3 - - + -
403D LEU* 3.9 13.0 - - + -
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D MET* 3.8 29.6 - - + -
158D THR* 3.1 21.2 + - + +
159D ALA* 3.6 6.7 - - - +
160D ARG 3.3 0.4 - - - -
161D VAL* 1.3 78.1 - - - +
163D ASP* 1.3 60.1 + - - +
165D ALA* 4.5 2.2 - - - +
166D SER* 2.8 57.6 + - - +
168D ILE* 3.8 17.7 - - + +
187D LEU* 5.2 3.4 - - + -
191D ILE* 3.8 31.6 - - + -
343D LEU* 4.0 23.3 - - + -
358D ILE* 4.8 7.5 - - + +
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Residues in contact with ASP 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D ARG* 3.4 25.7 + - - +
145D LEU 4.6 0.9 - - - +
146D ARG* 4.3 2.4 - - - +
147D MET* 3.3 28.8 + - - +
148D GLU* 2.9 37.5 + - + +
159D ALA 2.9 18.3 + - - +
160D ARG* 3.8 4.8 - - - +
161D VAL 3.3 0.2 - - - -
162D LEU* 1.3 78.2 - - - +
164D LEU* 1.3 65.2 + - + +
166D SER 4.5 2.2 - - - -
167D PRO* 3.4 25.2 - - - +
168D ILE 5.2 0.7 + - - -
380D MET* 3.5 10.0 - - + +
409D ASN* 5.4 2.5 - - - +
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Residues in contact with LEU 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ARG 3.2 16.1 + - - +
161D VAL* 3.9 4.9 - - - +
163D ASP* 1.3 78.6 - - + +
165D ALA* 1.3 61.4 + - - +
167D PRO* 5.1 0.2 - - - +
360D TYR* 3.3 26.4 + - + +
368D GLU* 5.6 0.9 - - - +
380D MET* 4.0 32.1 - - + +
383D LEU* 4.0 21.1 - - + -
384D ARG* 4.0 5.4 + - - -
399D LEU* 4.5 17.0 - - + -
403D LEU* 4.5 11.4 - - + -
409D ASN* 3.5 25.1 - - + +
412D PHE* 5.5 1.1 - - + -
413D PHE* 3.6 30.1 - - + -
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Residues in contact with ALA 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D VAL* 2.9 18.8 + - + +
162D LEU* 4.2 2.7 - - - +
164D LEU* 1.3 78.2 - - - +
166D SER* 1.3 61.8 + - - +
167D PRO* 3.9 6.0 - - - +
343D LEU* 4.9 5.4 - - + -
358D ILE* 5.1 2.9 - - + -
360D TYR* 3.6 21.8 - - + -
363D SER* 4.0 20.0 - - - +
364D GLY* 3.3 11.6 - - - -
365D THR 4.2 0.5 + - - -
368D GLU* 4.7 1.9 - - - +
384D ARG* 2.8 25.4 + - - +
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Residues in contact with SER 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D LEU* 2.8 31.1 + - - +
165D ALA* 1.3 75.2 - - - +
167D PRO* 1.3 68.4 - - - +
168D ILE* 3.4 11.1 + - - +
341D MET* 3.7 24.1 - - - -
342D GLU 5.6 0.4 - - - -
343D LEU* 3.8 23.5 - - - +
363D SER* 5.4 0.2 - - - -
364D GLY 4.2 7.4 - - - -
365D THR* 3.3 15.3 - - - -
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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