Contacts of the helix formed by residues 158 - 167 (chain H) 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 PHE 158 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76G ASN* 3.7 13.9 + - - +
81G TYR* 3.8 22.6 - + - +
43H LEU* 3.3 24.9 - - + +
79H PHE* 4.1 9.9 - + + -
113H VAL* 3.6 35.9 - - + -
115H LEU* 3.6 41.5 - - + -
119H SER* 4.2 5.8 - - - -
120H TYR 4.8 1.6 - - - -
121H HIS* 3.3 33.4 - + + -
154H ALA 4.3 3.1 - - - -
155H LEU* 3.2 31.2 + - + +
156H ARG 3.0 1.8 + - - -
157H SER* 1.3 78.0 - - - +
159H GLY* 1.3 57.1 + - - +
162H LEU* 3.7 17.0 - - + -
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Residues in contact with GLY 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G ASN* 4.8 2.2 - - - -
76G ASN* 3.9 11.7 - - - -
43H LEU* 4.0 10.3 - - - +
155H LEU 4.6 0.4 + - - -
156H ARG 3.3 6.5 + - - +
157H SER 3.4 1.2 - - - -
158H PHE* 1.3 80.9 - - - +
160H ASN* 1.3 67.4 + - - -
161H ALA 3.3 2.9 - - - -
162H LEU* 3.3 9.6 + - - +
163H GLY 3.6 0.7 + - - -
164H ASN* 3.2 24.1 + - - +
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Residues in contact with ASN 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G HIS* 5.7 0.9 - - - -
73G ASN* 3.4 34.2 + - - +
43H LEU 3.2 4.9 + - - -
44H ARG* 3.6 23.2 + - - +
45H GLN 3.6 14.6 - - - +
46H ARG* 4.4 12.2 + - + +
47H LEU* 3.1 12.8 - - - +
159H GLY* 1.3 72.7 - - - -
161H ALA* 1.3 58.5 + - - +
163H GLY 2.9 17.7 + - - -
164H ASN* 3.4 11.3 + - - +
165H CYS* 3.5 34.0 + - + +
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Residues in contact with ALA 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G LYS* 4.5 14.6 - - + -
42H ALA 3.5 24.5 - - - +
43H LEU* 3.1 21.8 + - + +
45H GLN 3.1 13.9 + - - +
47H LEU* 3.5 22.2 - - - +
74H LEU* 3.5 17.2 - - - +
78H MET* 4.6 7.4 - - + -
159H GLY 3.3 0.6 - - - -
160H ASN* 1.3 75.8 - - - +
162H LEU* 1.3 58.6 + - - +
163H GLY 3.4 0.2 - - - -
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Residues in contact with LEU 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H LEU* 4.1 11.9 - - + +
66H ILE* 5.1 0.2 - - - -
71H VAL* 4.1 24.8 - - + +
74H LEU* 3.7 21.8 - - + +
75H ALA* 3.5 35.9 - - + +
78H MET* 4.6 3.4 - - + -
79H PHE* 3.5 32.1 - - + -
152H LYS 4.8 0.5 - - - +
155H LEU* 3.5 22.6 - - + +
156H ARG* 4.1 13.1 + - - +
158H PHE* 3.7 23.8 - - + -
159H GLY 3.3 6.5 + - - +
160H ASN 3.1 0.8 - - - -
161H ALA* 1.3 77.8 - - - +
163H GLY* 1.3 56.8 + - - +
164H ASN 3.8 0.9 - - - -
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Residues in contact with GLY 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H LEU* 4.2 2.0 - - - +
66H ILE* 3.8 23.3 - - - -
156H ARG* 3.7 17.1 + - - +
160H ASN 2.9 7.5 + - - -
161H ALA 3.4 1.0 + - - -
162H LEU* 1.3 81.4 - - - +
164H ASN* 1.3 64.6 + - - +
165H CYS 3.3 2.7 - - - -
166H ILE* 3.1 25.3 - - - +
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Residues in contact with ASN 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G HIS* 3.1 28.9 + - - +
72G ILE* 3.1 40.0 - - - +
73G ASN* 3.2 21.2 + - - -
156H ARG* 3.5 15.7 + - - +
159H GLY 3.2 26.0 + - - +
160H ASN* 3.4 4.7 + - - +
162H LEU 3.8 0.4 - - - -
163H GLY* 1.3 78.9 - - - +
165H CYS* 1.3 63.3 + - - +
166H ILE 3.2 1.0 + - - -
167H LEU* 3.2 24.1 + - - +
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Residues in contact with CYS 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G HIS* 5.9 0.4 - - - -
46H ARG* 3.9 18.4 - - + +
47H LEU* 3.5 46.4 - - - -
52H ILE* 5.7 0.9 - - - -
160H ASN* 3.5 27.5 + - + +
163H GLY 4.8 0.9 - - - -
164H ASN* 1.3 72.8 - - - +
166H ILE* 1.3 65.5 + - - +
167H LEU 3.0 5.6 - - - -
168H ASP* 2.9 22.1 + - - +
171H TYR* 3.3 31.3 - - + -
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Residues in contact with ILE 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H ILE* 3.7 33.0 - - + -
64H CYS* 3.8 39.0 - - + +
65H TYR* 4.4 7.4 - - - +
66H ILE* 4.6 13.5 - - + -
156H ARG* 4.5 15.7 - - - +
163H GLY* 3.1 24.1 + - - +
164H ASN 3.1 1.0 - - - -
165H CYS* 1.3 79.4 - - - +
167H LEU* 1.3 74.5 + - + +
168H ASP 3.4 0.4 + - - -
171H TYR* 4.3 6.5 - - + -
172H LEU* 3.9 24.8 - - + +
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Residues in contact with LEU 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G GLU* 4.9 1.0 - - - +
68G GLY* 5.3 1.8 - - - -
69G HIS* 3.8 30.7 + - + +
72G ILE* 5.5 4.5 - - + -
156H ARG* 4.2 30.7 - - - +
164H ASN* 3.7 25.1 - - - +
165H CYS 2.9 1.4 + - - -
166H ILE* 1.3 89.9 - - + +
168H ASP* 1.3 60.4 + - - +
169H LYS* 3.4 11.3 + - - +
172H LEU* 5.6 1.3 - - - +
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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