Contacts of the helix formed by residues 168 - 177 (chain B) in PDB entry 5XRZ
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 ASP 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A HIS* 3.6 28.1 - - + +
70A ARG* 4.4 8.2 + - - -
186A VAL* 4.5 2.9 - - - +
46B ARG* 3.4 24.2 + - - +
165B CYS* 2.9 21.6 + - + +
167B LEU* 1.3 74.3 - - - +
169B LYS* 1.3 68.3 + - - +
170B ASP* 3.8 16.7 + - - +
171B TYR* 3.0 26.7 + - + +
172B LEU* 3.1 13.8 + - - +
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Residues in contact with LYS 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 4.4 12.3 + - - -
67A GLU* 3.7 35.1 + - - +
69A HIS* 5.1 1.0 + - - -
167B LEU 3.4 7.6 + - - +
168B ASP* 1.3 75.3 + - - +
170B ASP* 1.3 59.6 + - - +
172B LEU* 3.2 13.9 + - + +
173B ARG* 2.9 35.9 + - + +
2L T 5.5 7.9 - - - +
3L T 5.4 11.7 - - - -
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Residues in contact with ASP 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 4.6 10.4 + - - -
183A PRO* 3.6 13.1 - - - +
184A LEU* 3.6 29.9 + - - +
186A VAL* 3.6 20.4 - - + -
168B ASP* 3.2 13.2 + - - +
169B LYS* 1.3 81.0 - - - +
171B TYR* 1.3 56.8 + - - +
173B ARG* 3.0 29.0 + - - +
174B SER* 2.9 33.1 + - - -
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Residues in contact with TYR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 3.8 10.3 - - - +
188A LEU* 3.6 19.5 - - + -
46B ARG* 3.5 33.0 - - + +
47B LEU* 2.3 47.1 + - - +
52B ILE* 3.9 9.5 - - + +
165B CYS* 3.1 42.8 - - + +
166B ILE* 4.5 4.9 - - - -
168B ASP* 3.0 21.3 + - + +
170B ASP* 1.3 78.5 - - - +
172B LEU* 1.3 63.6 + - + +
174B SER* 3.3 2.9 + - - -
175B LEU* 2.9 55.4 + - + +
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Residues in contact with LEU 172 (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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64B CYS* 3.9 40.2 - - + +
166B ILE* 3.9 25.6 - - + +
167B LEU 5.9 0.2 - - - -
168B ASP 3.1 13.0 + - - +
169B LYS* 3.2 14.1 + - + +
171B TYR* 1.3 79.8 - - + +
173B ARG* 1.3 65.4 + - - +
175B LEU* 3.0 23.6 + - + +
176B ASN* 3.0 30.9 + - - +
4L T 5.7 9.2 - - + +
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PRO* 3.7 18.3 + - - +
184A LEU 3.5 18.4 + - - -
185A GLU* 5.0 3.0 - - - +
186A VAL 5.9 0.2 - - - +
169B LYS* 2.9 20.6 + - + +
170B ASP* 3.0 34.6 + - - +
172B LEU* 1.3 74.8 - - + +
174B SER* 1.3 63.7 + - - +
176B ASN* 3.4 16.7 + - - +
177B LYS* 3.3 48.8 + - - +
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Residues in contact with SER 174 (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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185A GLU* 4.6 5.4 - - - +
186A VAL* 2.8 40.9 + - - -
188A LEU* 3.4 21.8 - - - +
170B ASP 2.9 18.0 + - - -
171B TYR 3.7 2.0 - - - -
173B ARG* 1.3 76.0 + - - +
175B LEU* 1.3 63.8 + - - +
177B LYS* 3.3 23.5 + - - +
178B LEU* 3.8 8.8 - - - +
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Residues in contact with LEU 175 (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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188A LEU* 3.7 16.8 - - + -
47B LEU 4.4 1.3 - - - +
48B GLY 4.4 0.7 - - - -
49B PRO* 3.9 39.9 - - + +
52B ILE* 3.6 23.6 - - + -
64B CYS* 5.8 0.9 - - - -
171B TYR* 2.9 47.7 + - + +
172B LEU* 3.0 25.8 + - + +
174B SER* 1.3 75.7 - - - +
176B ASN* 1.3 66.5 + - - +
177B LYS 3.3 0.7 + - - -
178B LEU* 3.4 18.3 + - - +
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Residues in contact with ASN 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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62B LYS* 4.6 20.6 - - - +
64B CYS* 5.5 7.9 - - - -
172B LEU* 3.0 26.1 + - - +
173B ARG* 3.7 10.5 - - - +
174B SER 3.4 0.2 - - - -
175B LEU* 1.3 77.1 - - - +
177B LYS* 1.3 58.0 + - + +
178B LEU 3.2 10.5 + - - +
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Residues in contact with LYS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLU* 4.9 16.4 + - + +
173B ARG* 3.3 44.9 - - - +
174B SER* 3.3 16.4 + - - +
175B LEU 3.1 1.4 - - - -
176B ASN* 1.3 78.1 - - + +
178B LEU* 1.3 65.1 + - - +
179B PRO* 4.7 0.7 - - - +
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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