Contacts of the helix formed by residues 170 - 178 (chain B) in PDB entry 5X6E
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 THR 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ASN 4.1 10.1 - - - +
169B LEU* 1.3 89.0 - - - +
171B MET* 1.3 63.5 + - - +
172B GLN* 3.1 12.0 + - - +
173B GLU* 2.7 34.8 + - + +
174B LEU* 3.3 15.2 + - - +
206B PHE* 5.8 1.8 - - - -
7C C 4.2 26.7 - - - +
8C G 3.2 15.3 - - - +
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Residues in contact with MET 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B THR* 1.3 70.2 - - - +
172B GLN* 1.3 68.5 + - - +
174B LEU* 3.5 2.7 + - - +
175B GLY 3.2 12.5 + - - -
183B SER* 4.2 14.8 - - - +
186B VAL* 3.3 26.7 - - + +
187B SER* 4.1 14.1 - - - -
190B ILE* 3.5 46.9 - - + -
201B TYR* 5.1 9.0 - - + -
206B PHE* 5.0 12.6 - - + -
8C G 2.6 46.7 + - + +
9C T 3.0 28.5 - - + +
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Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B THR* 3.2 8.7 - - - +
171B MET* 1.3 76.4 - - - +
173B GLU* 1.3 54.8 + - - +
175B GLY* 2.5 31.6 + - - -
176B TYR* 2.3 53.3 + - + +
181B ALA 3.8 11.6 + - - +
182B HIS* 4.0 0.8 - - - +
183B SER* 3.1 44.3 + - - +
186B VAL* 5.5 0.7 - - - -
7C C 6.1 3.1 - - - -
8C G 4.1 3.6 + - - +
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Residues in contact with GLU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LYS* 2.1 37.8 + - - -
59B ASN* 2.8 20.8 + - - +
62B TYR* 3.7 12.7 + - - +
88B ILE* 5.2 0.6 - - - +
168B ASN* 4.9 5.6 - - + +
169B LEU* 4.3 14.6 - - + -
170B THR* 2.7 32.9 + - + +
172B GLN* 1.3 73.1 - - - +
174B LEU* 1.3 60.3 + - - +
176B TYR* 3.5 16.5 + - - -
177B SER* 3.4 13.9 + - - -
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ILE* 4.1 14.1 - - + -
146B GLN* 3.8 27.6 - - + -
147B LEU* 4.3 24.5 - - + -
150B LEU* 4.8 8.1 - - + -
169B LEU* 4.1 19.4 - - + +
170B THR 3.3 14.7 + - - +
171B MET* 3.6 5.6 - - - +
172B GLN 2.8 4.6 + - - -
173B GLU* 1.3 76.2 - - - +
175B GLY* 1.3 61.7 + - - +
177B SER* 3.1 21.7 + - - +
178B SER* 3.2 6.6 + - - -
186B VAL* 4.2 7.0 - - + -
190B ILE* 3.5 31.9 - - + -
206B PHE* 4.9 7.0 - - + -
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Residues in contact with GLY 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ILE* 4.9 0.2 - - - -
171B MET 3.2 3.2 + - - -
172B GLN 2.5 17.5 + - - -
174B LEU* 1.3 74.7 - - - +
176B TYR* 1.3 55.1 + - - -
178B SER* 3.0 31.5 + - - -
180B ILE* 2.9 23.2 + - - +
186B VAL* 3.6 24.2 - - - +
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Residues in contact with TYR 176 (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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57B ILE* 3.3 61.2 - - + +
58B MET* 3.8 5.0 - - - +
59B ASN* 2.8 45.2 + - - +
172B GLN* 2.3 71.7 + - + +
173B GLU* 3.6 11.4 - - - +
174B LEU 3.2 0.2 - - - -
175B GLY* 1.3 78.0 - - - +
177B SER* 1.3 57.4 + - - +
178B SER 3.0 12.0 - - - +
180B ILE 4.2 7.2 - - - -
181B ALA* 4.8 12.4 + - + -
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Residues in contact with SER 177 (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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131A PHE* 4.4 2.1 - - - -
58B MET* 3.9 4.0 - - - +
59B ASN* 3.3 28.0 - - - +
62B TYR* 3.7 16.6 + - - -
130B LYS* 4.7 0.9 - - - -
134B PHE* 3.7 15.0 - - - -
146B GLN* 3.4 36.5 + - - +
169B LEU* 6.2 0.2 - - - +
173B GLU 3.4 12.0 + - - -
174B LEU* 3.1 15.1 + - - +
176B TYR* 1.3 78.2 - - - +
178B SER* 1.3 60.1 + - - +
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Residues in contact with SER 178 (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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135A SER* 4.8 1.6 - - - -
58B MET* 3.2 16.0 - - - +
134B PHE* 4.1 10.8 - - - -
142B SER* 3.8 26.0 + - - -
143B ILE* 3.3 23.2 - - - +
146B GLN* 4.5 3.1 - - - +
174B LEU 3.2 6.3 + - - -
175B GLY 3.0 13.3 + - - +
176B TYR* 3.0 16.1 - - - +
177B SER* 1.3 77.2 - - - +
179B GLY* 1.3 60.9 + - - -
180B ILE* 4.1 16.2 - - - -
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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