Contacts of the helix formed by residues 160 - 170 (chain G) in PDB entry 6CAJ
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 SER 160 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129G ALA* 3.4 22.4 - - - +
130G TYR* 3.5 17.8 - - - +
155G SER 3.9 4.7 + - - -
158G ASP* 2.8 21.9 + - - -
159G LEU* 1.3 72.8 - - - +
161G GLY* 1.3 64.1 + - - +
162G LYS 3.2 2.0 - - - -
163G LYS* 3.1 17.9 + - - +
164G MET 2.9 22.0 + - - -
209G LYS* 4.3 5.9 - - - -
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Residues in contact with GLY 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G ALA* 4.5 7.1 - - - +
152G VAL* 3.5 12.9 - - - +
153G THR 3.7 14.4 - - - -
154G GLU* 3.1 23.3 + - - -
160G SER* 1.3 76.3 + - - +
162G LYS* 1.3 59.7 + - - +
164G MET* 3.3 6.1 + - - +
165G ALA* 2.9 28.6 + - - +
177G VAL* 5.5 2.1 - - - +
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Residues in contact with LYS 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G GLU* 4.3 6.0 + - + +
156G GLN* 5.8 2.5 - - - +
159G LEU* 3.8 39.2 - - + +
160G SER* 3.2 1.2 - - - +
161G GLY* 1.3 77.5 - - - +
163G LYS* 1.3 56.5 + - - +
165G ALA* 3.4 7.0 + - - +
166G LYS* 2.9 29.0 + - + +
177G VAL* 5.2 18.8 - - + +
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Residues in contact with LYS 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G TYR* 3.6 41.8 - - + -
159G LEU 4.4 6.1 + - - +
160G SER* 3.1 22.0 + - - +
162G LYS* 1.3 77.8 - - - +
164G MET* 1.3 59.3 + - - +
166G LYS* 3.7 8.2 - - + +
167G ALA* 2.9 30.0 + - + +
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Residues in contact with MET 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G THR* 4.5 4.7 - - + -
128G HIS 4.3 7.4 - - - +
130G TYR* 3.6 43.9 - - - +
131G SER 4.3 2.7 - - - +
134G VAL* 3.8 28.0 - - + -
135G LEU* 4.3 20.9 - - + +
138G LEU* 4.3 17.5 - - + -
152G VAL* 4.2 19.1 - - + -
160G SER 2.9 13.5 + - - +
161G GLY* 3.5 10.8 - - - +
163G LYS* 1.3 76.9 - - - +
165G ALA* 1.3 56.5 + - - +
167G ALA* 3.4 1.6 + - - -
168G LEU* 2.9 42.2 + - + +
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Residues in contact with ALA 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G VAL* 4.6 6.5 - - + +
161G GLY 2.9 17.0 + - - +
162G LYS 3.7 4.3 - - - +
164G MET* 1.3 77.0 - - - +
166G LYS* 1.3 57.9 + - - +
169G CYS* 2.9 29.8 + - - +
175G VAL* 3.5 31.8 - - + +
177G VAL* 3.8 28.0 - - + -
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Residues in contact with LYS 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162G LYS* 2.9 19.8 + - + +
163G LYS* 3.7 10.3 - - + +
165G ALA* 1.3 78.1 - - - +
167G ALA* 1.3 64.3 + - + +
169G CYS* 3.4 6.6 + - + +
170G HIS* 3.2 28.4 + - + +
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Residues in contact with ALA 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G TYR* 4.1 10.5 - - + +
135G LEU* 3.8 30.9 - - + +
163G LYS* 2.9 18.5 + - + +
164G MET 3.9 2.7 - - - +
166G LYS* 1.3 79.7 - - + +
168G LEU* 1.3 59.0 + - - +
170G HIS* 3.9 8.0 + - - +
171G LEU* 3.7 16.6 + - - +
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Residues in contact with LEU 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G LEU* 5.2 1.5 - - + +
138G LEU* 3.8 25.1 - - + -
148G PHE* 6.0 0.2 - - + -
150G VAL* 3.7 40.4 - - + -
152G VAL* 4.6 4.3 - - + -
164G MET* 2.9 27.8 + - + +
165G ALA* 4.1 4.0 - - - +
167G ALA* 1.3 76.6 - - - +
169G CYS* 1.3 62.4 + - - +
170G HIS 3.3 0.7 - - - -
171G LEU* 3.2 46.5 + - + +
172G ASN 3.6 4.0 + - - -
173G VAL* 3.6 18.4 + - + +
175G VAL* 3.8 18.6 - - + -
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Residues in contact with CYS 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G ALA 2.9 18.8 + - - +
166G LYS* 3.4 8.9 + - + +
168G LEU* 1.3 74.5 - - - +
170G HIS* 1.3 63.2 + - - +
172G ASN* 3.3 13.0 + - - -
173G VAL 4.5 5.2 - - - -
175G VAL* 4.2 15.0 - - + +
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Residues in contact with HIS 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166G LYS* 3.2 21.5 + - + +
167G ALA* 4.0 9.0 - - - +
168G LEU 3.3 0.4 - - - -
169G CYS* 1.3 75.2 - - - +
171G LEU* 1.3 59.5 + - - +
172G ASN* 3.2 5.5 + - - +
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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