Contacts of the helix formed by residues 176 - 189 (chain A) in PDB entry 6GYS
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 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A THR* 5.5 7.9 - - + -
175A LEU* 1.3 78.6 - - - +
177A PRO* 1.3 62.7 - - - +
178A GLN* 3.6 11.6 + - - +
179A LEU* 2.8 29.6 + - + +
180A VAL* 2.5 34.2 + - - +
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Residues in contact with PRO 177 (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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175A LEU 4.2 2.9 - - - +
176A THR* 1.3 84.0 - - - +
178A GLN* 1.3 61.9 + - + +
180A VAL* 3.3 12.7 - - + +
181A ASP* 2.9 30.3 + - - +
257A SER* 6.5 0.4 - - - -
258A ILE* 5.5 3.6 - - + -
259A SER* 3.7 29.7 - - - +
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Residues in contact with GLN 178 (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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176A THR* 3.6 9.9 - - - +
177A PRO* 1.3 79.3 - - + +
179A LEU* 1.3 58.6 + - - +
181A ASP* 3.3 4.6 + - - +
182A LYS* 2.9 30.3 + - - +
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Residues in contact with LEU 179 (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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72A THR* 4.5 15.5 - - + +
73A TYR* 4.2 8.3 - - - +
121A THR* 4.3 1.6 - - - +
122A TYR* 3.4 55.0 - - + +
175A LEU* 3.7 31.4 - - + -
176A THR* 2.8 27.6 + - + +
178A GLN* 1.3 73.2 - - - +
180A VAL* 1.3 60.8 + - - +
182A LYS* 4.5 5.4 - - + -
183A CYS* 2.9 35.2 + - + +
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Residues in contact with VAL 180 (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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170A PHE* 5.0 2.8 - - + -
172A ILE* 4.2 18.6 - - + -
175A LEU* 3.4 21.9 - - + +
176A THR 2.5 23.2 + - - +
177A PRO* 3.3 16.8 - - + +
178A GLN 3.2 0.2 - - - -
179A LEU* 1.3 71.8 - - - +
181A ASP* 1.3 60.2 + - - +
183A CYS* 3.6 2.3 - - - +
184A LEU* 2.9 42.5 + - + +
259A SER* 3.7 35.0 - - - +
262A ARG* 4.2 5.2 - - + -
263A THR* 4.1 8.3 - - - +
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Residues in contact with ASP 181 (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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177A PRO 2.9 16.7 + - - +
178A GLN* 4.1 3.1 - - - +
180A VAL* 1.3 78.8 - - - +
182A LYS* 1.3 58.1 + - - +
184A LEU* 3.3 2.6 + - - -
185A SER* 2.9 28.4 + - - -
262A ARG* 2.9 46.3 + - + -
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Residues in contact with LYS 182 (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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122A TYR* 3.0 52.1 + - + -
125A ASN* 4.9 3.8 - - - +
178A GLN 2.9 18.1 + - - +
179A LEU* 4.2 5.6 - - - +
181A ASP* 1.3 75.4 - - - +
183A CYS* 1.3 60.7 + - - +
185A SER* 2.5 25.5 + - - +
186A ILE* 2.9 30.8 + - + +
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Residues in contact with CYS 183 (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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120A TRP* 4.5 12.3 - - - -
121A THR* 3.9 16.4 - - - -
122A TYR* 4.7 4.2 - - + +
127A LEU* 3.4 26.6 - - + +
170A PHE* 4.3 22.4 - - + -
175A LEU* 5.2 5.2 - - + -
179A LEU* 2.9 30.4 + - + +
180A VAL* 3.6 4.9 - - - +
182A LYS* 1.3 76.8 - - - +
184A LEU* 1.3 57.2 + - - +
187A LEU* 2.8 34.4 + - - +
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Residues in contact with LEU 184 (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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170A PHE* 3.6 28.3 - - + -
180A VAL* 2.9 26.3 + - + +
181A ASP 3.6 4.7 - - - +
182A LYS 3.2 0.2 - - - -
183A CYS* 1.3 75.6 - - - +
185A SER* 1.3 58.8 + - - +
187A LEU* 3.7 2.3 - - + +
188A GLU* 2.8 30.5 + - - +
193A PHE* 3.9 29.9 - - + -
262A ARG* 3.6 46.2 + - + +
263A THR* 4.4 3.1 - - - -
266A SER* 3.3 29.4 - - - +
270A MET* 6.1 0.2 - - + -
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Residues in contact with SER 185 (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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181A ASP* 2.9 13.9 + - - -
182A LYS* 2.5 31.1 + - - +
184A LEU* 1.3 75.2 - - - +
186A ILE* 1.3 63.1 + - - +
188A GLU* 3.2 7.6 + - - +
189A GLN* 3.0 30.2 + - - +
262A ARG* 5.0 4.2 - - - +
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Residues in contact with ILE 186 (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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122A TYR* 3.6 30.1 - - + +
126A GLU 4.9 3.6 - - - +
127A LEU* 3.7 30.2 - - + +
182A LYS* 2.9 36.3 + - + +
185A SER* 1.3 84.4 + - - +
187A LEU* 1.3 64.7 + - - +
189A GLN* 3.3 37.9 - - - +
190A LYS* 3.5 20.9 + - - +
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Residues in contact with LEU 187 (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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120A TRP* 3.8 40.2 - - + +
127A LEU* 4.0 7.3 - - + +
170A PHE* 5.0 10.8 - - + -
183A CYS* 2.8 20.6 + - - +
184A LEU* 3.8 5.4 - - + +
186A ILE* 1.3 76.3 - - - +
188A GLU* 1.3 57.7 + - - +
190A LYS* 2.8 22.6 - - - +
192A LEU* 3.5 46.7 + - + +
193A PHE* 3.5 32.3 - - + +
196A ILE* 4.5 5.6 - - + -
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Residues in contact with GLU 188 (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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184A LEU 2.8 17.3 + - - +
185A SER* 3.3 9.4 - - - +
186A ILE 3.2 0.4 - - - -
187A LEU* 1.3 74.4 - - - +
189A GLN* 1.3 57.5 + - - +
190A LYS 2.9 17.1 - - - +
193A PHE* 3.1 27.3 - - - -
262A ARG* 5.8 4.5 + - - +
266A SER* 5.8 2.8 - - - -
269A SER* 5.2 6.4 + - - -
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Residues in contact with GLN 189 (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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185A SER 3.0 12.6 + - - +
186A ILE* 3.3 49.6 - - - +
188A GLU* 1.3 76.6 - - - +
190A LYS* 1.3 67.4 + - + +
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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