Contacts of the helix formed by residues 168 - 177 (chain P) in PDB entry 5XS0
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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69O HIS* 3.9 24.1 - - + +
70O ARG* 4.4 6.5 + - - -
186O VAL* 4.1 5.7 - - - +
46P ARG* 3.4 28.1 + - - +
164P ASN 4.3 0.6 + - - -
165P CYS* 3.0 11.7 + - - +
167P LEU* 1.3 77.5 - - - +
169P LYS* 1.3 62.9 + - - +
170P ASP* 3.3 16.9 + - - +
171P TYR* 3.1 24.5 + - + +
172P LEU* 2.9 29.9 + - - +
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Residues in contact with LYS 169 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65O TYR* 5.0 4.9 + - - -
67O GLU* 3.3 31.9 + - - +
69O HIS* 5.2 0.4 + - - -
167P LEU 4.2 8.5 - - - +
168P ASP* 1.3 75.1 + - - +
170P ASP* 1.3 62.1 + - - +
172P LEU* 3.2 14.7 + - + +
173P ARG* 3.0 35.8 + - + +
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Residues in contact with ASP 170 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70O ARG* 4.4 12.0 + - - -
183O PRO* 3.5 13.1 - - - +
184O LEU* 3.3 36.1 + - - +
186O VAL* 3.7 14.6 - - + +
168P ASP* 3.2 11.8 + - - +
169P LYS* 1.3 77.4 - - - +
171P TYR* 1.3 60.0 + - - +
173P ARG* 2.9 27.1 + - - +
174P SER* 2.9 33.3 + - - -
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Residues in contact with TYR 171 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186O VAL* 3.6 10.1 - - - +
188O LEU* 3.7 17.3 - - + -
46P ARG* 3.5 38.1 - - + +
47P LEU* 2.3 38.2 + - - +
52P ILE* 3.6 15.0 - - + +
165P CYS* 3.0 32.1 - - + -
166P ILE* 4.3 3.8 - - - -
168P ASP* 3.1 24.6 + - + +
170P ASP* 1.3 79.7 - - - +
172P LEU* 1.3 68.8 + - + +
174P SER* 3.4 2.3 + - - -
175P LEU* 2.9 57.0 + - + +
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Residues in contact with LEU 172 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64P CYS* 4.0 35.4 - - + +
166P ILE* 3.8 23.1 - - + +
167P LEU 5.4 1.1 - - - -
168P ASP 2.9 16.3 + - - +
169P LYS* 3.6 16.2 - - + +
170P ASP 3.2 0.2 - - - -
171P TYR* 1.3 92.8 - - + +
173P ARG* 1.3 64.9 + - + +
175P LEU* 3.1 11.0 + - + +
176P ASN* 2.9 34.3 + - - +
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Residues in contact with ARG 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183O PRO* 3.7 21.1 + - - +
184O LEU 3.8 7.5 + - - -
185O GLU* 5.2 6.7 - - - +
169P LYS* 3.0 18.6 + - + +
170P ASP* 2.9 37.5 + - - +
172P LEU* 1.3 77.3 - - + +
174P SER* 1.3 63.7 + - - +
176P ASN* 3.2 7.7 + - - +
177P LYS* 3.2 58.1 + - - +
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Residues in contact with SER 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185O GLU* 4.0 10.0 - - - +
186O VAL* 3.1 39.5 + - - -
188O LEU* 3.4 14.0 - - - +
170P ASP 2.9 17.0 + - - -
171P TYR 3.8 4.0 - - - -
173P ARG* 1.3 78.3 + - - +
175P LEU* 1.3 57.3 + - - +
177P LYS* 4.1 11.7 + - - +
178P LEU* 3.2 25.6 + - - +
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Residues in contact with LEU 175 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188O LEU* 3.8 14.8 - - + -
47P LEU 4.6 0.4 - - - +
48P GLY 4.6 0.4 - - - -
49P PRO* 3.8 40.1 - - + +
52P ILE* 3.6 26.2 - - + -
64P CYS* 5.7 1.3 - - - -
171P TYR* 2.9 54.6 + - + +
172P LEU* 3.1 13.8 + - + +
174P SER* 1.3 78.1 - - - +
176P ASN* 1.3 65.8 + - - +
177P LYS 3.3 0.2 - - - -
178P LEU* 3.3 19.0 + - + +
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Residues in contact with ASN 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62P LYS* 3.5 35.0 - - - +
64P CYS* 5.5 6.1 - - - -
172P LEU* 2.9 26.7 + - - +
173P ARG* 3.2 7.3 + - - +
175P LEU* 1.3 78.2 - - - +
177P LYS* 1.3 62.7 + - + +
178P LEU 3.1 9.8 + - - +
180P ARG* 6.0 0.7 - - - +
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Residues in contact with LYS 177 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185O GLU* 4.5 16.0 + - - +
173P ARG* 3.2 49.1 + - - +
174P SER* 4.4 9.8 + - - +
175P LEU 3.3 0.4 - - - -
176P ASN* 1.3 76.1 - - + +
178P LEU* 1.3 60.1 + - - +
179P PRO* 4.0 2.4 - - - +
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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