Contacts of the helix formed by residues 162 - 173 (chain A) in PDB entry 6I4X
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 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A PRO* 1.3 78.1 - - - +
163A LEU* 1.3 59.2 + - - +
164A GLN* 3.6 6.4 + - - +
165A HIS* 3.0 25.9 + - - +
166A LEU* 3.0 26.9 + - - +
190A TYR* 4.2 2.6 + - - -
76C TYR* 3.2 7.0 - - - -
112C CYS* 3.3 16.2 - - - -
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A SER* 1.3 73.6 - - - +
164A GLN* 1.3 62.7 + - - +
166A LEU* 3.3 3.1 + - + -
167A CYS* 3.0 23.6 + - - -
72C LYS 5.2 0.4 - - - +
73C VAL* 4.1 14.4 - - + -
76C TYR* 3.3 45.6 + - + -
93C PHE* 4.1 13.5 - - + -
95C ILE* 4.2 7.0 - - + -
103C LEU* 3.8 44.0 - - + -
107C ALA* 3.8 17.5 - - + -
112C CYS* 2.8 25.9 + - - +
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Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A SER* 3.2 5.9 - - - +
163A LEU* 1.3 77.2 - - - +
165A HIS* 1.3 61.6 + - - +
167A CYS* 3.2 5.4 + - - +
168A ARG* 3.1 21.5 + - - +
187A LEU* 5.0 1.2 - - - +
190A TYR* 3.6 32.2 - - + +
104C LEU* 3.9 9.3 - - + +
107C ALA* 3.4 29.2 + - + +
108C ASN* 3.3 36.6 + - + +
111C ASP* 3.8 23.4 + - - +
112C CYS 3.3 13.1 + - - +
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Residues in contact with HIS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLN* 3.3 26.4 + - - +
46A THR 3.7 12.7 + - - -
157A TYR* 5.4 0.2 - + - -
161A PRO* 4.2 20.0 - - + -
162A SER* 3.0 24.8 + - - +
164A GLN* 1.3 76.9 - - - +
166A LEU* 1.3 61.5 + - - +
168A ARG* 3.0 27.7 + - - +
169A LEU* 3.1 42.2 + - + +
190A TYR* 3.3 10.7 + - - +
194A TYR* 3.6 34.9 + + - -
198A VAL* 5.7 0.2 + - - -
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A TYR* 4.9 6.5 - - + +
161A PRO* 3.6 26.5 - - + +
162A SER 3.0 16.2 + - - +
163A LEU* 3.7 7.0 - - - +
164A GLN 3.2 0.4 - - - -
165A HIS* 1.3 77.8 - - - +
167A CYS* 1.3 59.8 + - - +
169A LEU* 3.5 18.2 + - + +
170A THR* 3.2 24.4 + - - -
76C TYR* 3.9 29.4 - - + -
79C TYR* 4.4 8.3 - - + +
93C PHE* 3.8 36.8 - - + +
95C ILE* 3.8 13.3 - - + +
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Residues in contact with CYS 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 3.0 24.8 + - - -
164A GLN 3.2 6.9 + - - +
166A LEU* 1.3 73.7 - - - +
168A ARG* 1.3 61.4 + - - +
170A THR* 3.2 5.2 + - - +
171A ILE* 2.8 35.9 + - - +
95C ILE* 4.0 7.2 - - - -
100C ALA* 4.0 8.5 - - - +
103C LEU* 3.6 33.7 - - - -
104C LEU* 3.6 43.7 - - + -
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Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLN* 3.1 22.6 + - - -
164A GLN 3.1 12.2 + - - +
165A HIS* 3.0 34.1 + - - +
167A CYS* 1.3 76.1 - - - +
169A LEU* 1.3 56.2 + - - +
171A ILE* 3.3 1.4 + - - +
172A ASN* 2.8 40.5 + - - +
190A TYR* 2.6 73.3 + - + -
191A LEU* 3.6 30.9 - - + +
193A GLU* 4.2 6.7 - - - +
194A TYR* 3.3 49.1 - - + +
104C LEU* 5.0 0.6 - - + +
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A TYR* 3.5 24.2 - - + +
165A HIS* 3.1 38.5 + - + +
166A LEU* 3.8 16.4 - - + +
167A CYS 3.2 0.2 - - - -
168A ARG* 1.3 76.8 - - - +
170A THR* 1.3 62.3 + - - +
172A ASN* 3.3 4.8 + - - +
173A LYS* 3.1 41.3 + - - +
194A TYR* 3.9 11.2 - - + -
196A PHE 3.9 8.7 - - - +
197A GLN 3.8 15.7 - - - +
198A VAL* 3.7 31.4 - - - +
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Residues in contact with THR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU 3.2 12.5 + - - -
167A CYS 3.2 7.9 + - - -
169A LEU* 1.3 78.9 - - - +
171A ILE* 1.3 62.0 + - - +
173A LYS* 3.4 19.8 + - - +
174A CYS* 3.4 16.6 - - - -
93C PHE 5.5 0.9 + - - -
95C ILE* 3.3 42.8 + - + +
97C PRO* 4.4 13.9 - - + -
100C ALA* 3.9 18.4 - - + -
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Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A CYS 2.8 21.7 + - - +
168A ARG* 3.8 4.7 - - - +
170A THR* 1.3 74.6 - - - +
172A ASN* 1.3 68.4 + - - +
174A CYS* 3.1 15.7 + - - +
175A THR* 3.2 22.5 + - + +
181A LEU* 4.1 15.9 - - + -
191A LEU* 4.1 23.3 - - + -
103B MET* 5.0 7.4 - - + -
100C ALA* 4.0 24.5 - - + +
101C LEU* 4.1 20.0 - - + -
104C LEU* 3.6 30.7 - - + -
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Residues in contact with ASN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ARG* 2.8 31.2 + - - +
169A LEU 3.3 4.2 + - - +
171A ILE* 1.3 82.6 - - - +
173A LYS* 1.3 61.1 + - - +
174A CYS 3.5 0.5 + - - -
175A THR 3.6 15.8 + - - +
176A GLY* 5.6 0.2 - - - -
178A ILE* 6.1 0.5 - - - +
191A LEU* 4.6 8.0 - - - +
194A TYR* 2.8 30.8 + - - +
195A LYS* 3.3 15.2 - - - +
196A PHE 2.8 32.0 + - - +
197A GLN* 3.7 16.3 + - + +
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LYS* 6.2 3.8 - - - +
169A LEU* 3.1 34.9 + - - +
170A THR* 3.8 12.6 + - + +
171A ILE 3.2 0.6 - - - -
172A ASN* 1.3 77.8 - - - +
174A CYS* 1.3 61.7 + - - +
197A GLN* 3.3 51.1 + - + +
92C GLU* 5.6 4.8 + - - -
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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