Contacts of the helix formed by residues 157 - 170 (chain H) in PDB entry 5T35
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 157 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76G TYR* 3.2 7.6 - - - +
112G CYS* 3.5 17.9 - - - +
155H VAL 3.8 0.6 + - - +
156H TYR* 1.3 76.4 - - - +
158H LEU* 1.3 64.8 + - - +
159H LYS* 3.8 3.3 + - - +
160H GLU* 3.0 27.5 + - - +
161H ARG* 3.0 22.3 + - - +
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Residues in contact with LEU 158 (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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72G LYS 5.9 0.2 - - - +
73G VAL* 4.3 15.7 - - + -
76G TYR* 3.4 33.4 + - + -
93G PHE* 4.2 21.3 - - + -
95G ILE* 4.5 3.8 - - + -
103G LEU* 3.9 39.5 - - + -
107G ALA* 3.8 18.8 - - + -
112G CYS* 2.9 32.6 + - - +
157H THR* 1.3 71.5 - - - +
159H LYS* 1.3 56.3 + - - +
161H ARG* 3.4 3.8 + - + +
162H CYS* 2.9 40.6 + - - -
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Residues in contact with LYS 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G LEU* 3.8 7.7 - - + +
107G ALA* 3.6 22.3 - - + +
108G ASN* 4.6 7.0 - - + +
112G CYS 3.2 15.0 + - - +
157H THR* 3.2 4.0 - - - +
158H LEU* 1.3 77.8 - - - +
160H GLU* 1.3 57.8 + - - +
162H CYS* 3.2 5.8 + - - +
163H LEU* 2.9 35.1 + - + +
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Residues in contact with GLU 160 (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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126H ASP* 4.7 0.2 - - - +
156H TYR* 4.4 11.0 - - + -
157H THR* 3.0 26.6 + - - +
159H LYS* 1.3 76.8 - - - +
161H ARG* 1.3 56.9 + - - +
163H LEU* 3.3 21.4 + - - +
164H GLN* 3.0 43.8 + - - +
167H ARG* 3.2 27.4 + - - -
192H PRO* 4.5 8.1 - - - +
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Residues in contact with ARG 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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76G TYR* 6.0 1.8 - - + -
92G GLU* 3.4 28.7 + - - +
93G PHE* 3.0 39.7 + - + +
94G PRO* 4.9 3.6 - - - +
95G ILE* 3.9 16.3 - - + +
82H ARG* 3.6 10.3 - - - +
156H TYR* 4.4 15.0 - - + +
157H THR 3.0 18.4 + - - +
158H LEU* 3.7 7.9 - - + +
160H GLU* 1.3 74.6 - - - +
162H CYS* 1.3 64.5 + - - +
164H GLN* 2.8 48.2 + - - +
165H VAL* 3.3 45.4 + - - +
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Residues in contact with CYS 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ILE* 3.7 19.1 - - - -
100G ALA* 4.3 5.6 - - - +
103G LEU* 3.7 28.7 - - - -
104G LEU* 3.6 40.6 - - + -
158H LEU* 2.9 27.5 + - - +
159H LYS 3.6 4.5 - - - +
161H ARG* 1.3 73.7 - - - +
163H LEU* 1.3 64.4 + - - +
165H VAL* 3.4 3.0 + - - +
166H VAL* 3.1 30.7 + - - +
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Residues in contact with LEU 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G LEU* 3.7 21.3 - - + -
159H LYS* 2.9 19.7 + - + +
160H GLU* 3.4 26.9 - - - +
162H CYS* 1.3 77.3 - - - +
164H GLN* 1.3 56.6 + - - +
166H VAL* 3.8 1.7 - - - +
167H ARG* 2.9 62.5 + - - +
184H LEU* 4.8 1.8 - - + +
187H ASP* 4.0 20.9 - - + +
188H LEU* 3.8 37.8 - - + +
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Residues in contact with GLN 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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82H ARG* 3.1 11.1 + - - -
124H THR* 6.0 1.7 - - - +
126H ASP* 3.4 36.3 + - - +
156H TYR* 3.4 39.4 - - - -
160H GLU* 3.0 29.2 + - - +
161H ARG* 2.8 40.8 + - - +
162H CYS 3.3 0.2 - - - -
163H LEU* 1.3 76.8 - - - +
165H VAL* 1.3 57.7 + - - +
167H ARG* 3.5 11.0 + - - +
168H SER* 3.1 26.7 + - - -
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Residues in contact with VAL 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ILE* 4.1 32.1 - - + +
97G PRO* 5.3 1.6 - - + -
100G ALA* 4.3 14.8 - - + -
161H ARG* 3.3 45.7 + - - +
162H CYS* 3.9 4.9 - - - +
163H LEU 3.3 0.4 - - - -
164H GLN* 1.3 72.3 - - - +
166H VAL* 1.3 66.7 + - - +
168H SER* 2.7 26.2 + - - +
169H LEU* 3.3 24.5 + - + +
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Residues in contact with VAL 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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103F MET* 5.2 4.0 - - + -
100G ALA* 4.1 30.3 - - + +
101G LEU* 4.6 11.9 - - + -
104G LEU* 4.4 11.2 - - + -
162H CYS 3.1 19.3 + - - +
163H LEU* 3.9 3.6 - - - +
165H VAL* 1.3 74.5 - - - +
167H ARG* 1.3 64.4 + - - +
169H LEU* 3.1 6.9 + - - +
170H VAL* 3.1 39.6 + - + +
175H TYR* 5.6 0.2 - - + -
178H LEU* 4.2 15.9 - - + -
188H LEU* 3.9 21.1 - - + -
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Residues in contact with ARG 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H ASP* 4.6 0.6 + - - -
160H GLU* 3.2 23.4 + - - -
163H LEU* 2.9 48.6 + - - +
164H GLN* 3.6 17.0 - - - +
166H VAL* 1.3 76.7 - - - +
168H SER* 1.3 60.7 + - - +
169H LEU 3.2 1.2 + - - -
170H VAL 3.3 15.9 - - - +
175H TYR* 3.6 22.1 + - - +
187H ASP 3.2 24.0 + - - -
188H LEU* 3.2 23.5 + - + +
190H ASP 3.7 12.5 + - - -
191H HIS* 3.4 20.8 - - - +
192H PRO* 3.7 24.0 - - - +
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Residues in contact with SER 168 (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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124H THR* 6.0 6.1 - - - -
164H GLN 3.1 13.8 + - - -
165H VAL* 2.7 24.0 + - - +
167H ARG* 1.3 75.2 - - - +
169H LEU* 1.3 66.6 + - - +
170H VAL 3.7 0.2 - - - -
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Residues in contact with LEU 169 (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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102F VAL 3.7 12.8 - - - +
103F MET* 4.0 42.9 - - + +
104F LYS* 5.4 0.7 - - - +
97G PRO* 4.1 28.7 - - + -
100G ALA* 5.4 0.7 - - + -
165H VAL* 3.3 33.4 + - + +
166H VAL* 3.1 5.6 + - - +
168H SER* 1.3 85.2 - - - +
170H VAL* 1.3 65.6 + - + +
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Residues in contact with VAL 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F VAL* 4.6 7.0 - - + +
103F MET* 3.7 25.1 - - + -
166H VAL* 3.1 28.8 + - + +
167H ARG 3.3 15.1 + - - +
168H SER 3.7 0.2 - - - -
169H LEU* 1.3 86.6 - - + +
171H LYS* 1.3 75.7 + - - +
172H PRO* 3.7 2.8 - - - +
174H ASN* 3.8 19.5 - - + +
175H TYR* 3.3 28.7 + - + +
178H LEU* 4.3 14.8 - - + -
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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