Contacts of the helix formed by residues 162 - 182 (chain A) in PDB entry 2G1X
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 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PRO* 3.9 8.8 - - - +
160A LYS* 3.8 3.9 + - - -
161A ARG* 1.3 74.4 - - - +
163A PRO* 1.3 81.9 - - - +
164A LYS* 3.1 29.4 + - + +
165A ARG* 3.2 35.1 + - + +
166A ALA 3.3 7.4 + - - -
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Residues in contact with PRO 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A HIS* 4.3 31.2 - - + +
83A PRO* 5.2 0.9 - - + -
86A TYR* 3.8 28.4 - - + +
161A ARG 4.6 1.3 - - - +
162A THR* 1.3 92.9 - - - +
164A LYS* 1.3 64.5 + - - +
166A ALA* 3.1 18.4 + - + +
167A ALA* 3.2 11.1 + - - +
280A GLU* 4.8 13.0 - - - +
302A LYS* 5.4 3.6 - - - +
303A LYS* 4.8 7.4 - - - +
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Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A THR* 3.1 16.5 - - + +
163A PRO* 1.3 77.3 - - + +
165A ARG* 1.3 59.8 + - + +
167A ALA* 2.9 23.6 + - - +
168A VAL* 3.1 10.4 + - - +
279A SER* 5.5 4.9 - - - -
280A GLU* 3.9 37.1 + - - +
302A LYS* 4.8 17.8 - - + +
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Residues in contact with ARG 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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158A SER* 4.2 5.2 + - - +
159A ALA* 3.7 21.0 + - - +
160A LYS 3.1 25.1 + - - -
161A ARG* 3.4 42.1 - - - +
162A THR* 3.2 25.9 + - + +
164A LYS* 1.3 75.5 - - + +
166A ALA* 1.3 64.1 + - - +
168A VAL* 2.7 34.0 - - + +
169A MET* 3.2 3.1 + - - +
251A LEU* 3.3 11.7 - - + +
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Residues in contact with ALA 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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83A PRO* 3.6 19.7 - - + -
86A TYR* 3.6 36.6 - - + -
162A THR 3.3 3.6 + - - -
163A PRO* 3.1 13.0 + - + +
165A ARG* 1.3 80.0 - - - +
167A ALA* 1.3 59.0 + - - +
169A MET 3.3 1.0 + - - -
170A ILE* 2.9 26.3 + - - +
251A LEU* 3.0 12.9 - - - +
252A THR* 3.3 7.9 - - - +
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Residues in contact with ALA 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 PRO 3.2 7.2 + - - +
164A LYS* 2.9 12.2 + - - +
166A ALA* 1.3 76.9 - - - +
168A VAL* 1.3 59.6 + - - +
170A ILE* 2.7 39.9 - - + +
171A ALA* 2.8 7.1 + - - +
255A GLN* 3.0 31.0 + - - +
302A LYS* 4.2 17.3 - - + +
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Residues in contact with VAL 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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164A LYS 3.1 7.7 + - - +
165A ARG* 2.7 35.6 + - + +
167A ALA* 1.3 75.4 - - - +
169A MET* 1.3 70.8 + - + +
171A ALA* 3.1 7.9 + - + +
172A LEU* 2.7 37.7 + - + +
255A GLN* 5.0 0.2 - - - +
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Residues in contact with MET 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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142A VAL* 3.3 34.5 - - + +
145A LEU* 4.4 21.3 - - + -
161A ARG* 4.2 11.7 - - - +
165A ARG 3.2 1.7 + - - +
167A ALA 3.2 0.2 - - - -
168A VAL* 1.3 96.8 - - + +
170A ILE* 1.3 52.0 + - - +
172A LEU* 3.4 10.7 - - - +
173A VAL* 2.8 39.3 + - - +
251A LEU* 2.9 49.4 - - + -
252A THR* 2.8 13.9 - - - +
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Residues in contact with ILE 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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86A TYR* 4.9 0.9 - - + -
90A SER* 5.3 0.2 + - - -
166A ALA 2.9 20.5 + - - +
167A ALA* 2.7 27.5 + - + +
169A MET* 1.3 75.8 - - - +
171A ALA* 1.3 65.5 + - - +
173A VAL* 3.2 5.9 + - - +
174A TRP* 3.1 20.7 + - + +
252A THR* 2.9 5.5 + - - -
253A ARG* 2.7 52.6 - - + +
254A ALA* 2.9 17.0 - - - +
255A GLN* 2.8 42.8 - - + +
302A LYS 4.6 4.7 - - - +
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Residues in contact with ALA 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 ALA 2.8 7.9 + - - +
168A VAL* 3.5 11.9 - - + +
170A ILE* 1.3 83.3 - - - +
172A LEU* 1.3 57.6 + - - +
174A TRP* 3.1 9.0 + - + +
175A VAL* 2.9 35.2 + - + +
255A GLN* 4.4 11.7 - - + +
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Residues in contact with LEU 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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138A LEU* 2.9 55.0 - - + +
141A CYS* 6.5 0.7 - - - -
142A VAL* 4.6 4.7 - - + -
168A VAL* 2.7 21.9 + - + +
169A MET* 3.4 15.9 - - - +
170A ILE 3.2 0.2 - - - -
171A ALA* 1.3 75.0 - - - +
173A VAL* 1.3 61.8 + - - +
175A VAL* 2.7 30.2 - - + +
176A PHE* 2.9 34.4 + - + -
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Residues in contact with VAL 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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90A SER* 5.2 5.8 - - - +
135A ALA* 2.9 43.7 - - + +
138A LEU* 2.9 33.4 - - + +
139A HIS* 3.8 12.3 - - + -
142A VAL* 4.0 0.2 - - + -
169A MET 2.8 27.1 + - - +
170A ILE 3.2 6.3 + - - +
172A LEU* 1.3 74.3 - - - +
174A TRP* 1.3 55.5 + - - +
176A PHE 3.4 0.2 + - - -
177A SER* 2.6 37.4 + - - +
252A THR* 3.1 16.8 - - + +
253A ARG 5.0 2.5 - - - +
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Residues in contact with TRP 174 (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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131A THR* 5.8 3.1 - - - -
135A ALA* 6.3 0.2 - - - -
170A ILE* 3.1 10.7 + - + +
171A ALA* 3.1 11.5 + - + +
173A VAL* 1.3 80.9 - - - +
175A VAL* 1.3 73.8 + - + +
177A SER* 3.5 6.1 - - - -
178A ILE* 2.8 80.9 + - + +
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Residues in contact with VAL 175 (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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171A ALA* 2.9 17.6 + - + +
172A LEU* 2.7 32.5 - - + +
174A TRP* 1.3 91.7 - - + +
176A PHE* 1.3 82.6 + - + +
178A ILE* 2.7 14.6 - - + +
179A SER* 2.7 29.7 + - - -
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Residues in contact with PHE 176 (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 THR* 3.8 3.1 + - - +
138A LEU* 2.9 21.3 - - + -
172A LEU* 2.9 61.0 + - + -
175A VAL* 1.3 89.7 - - + +
177A SER* 1.3 60.2 + - - +
179A SER* 3.4 10.8 + - - -
180A ILE* 3.2 26.2 + - - +
215A GLY 5.9 3.6 - - - -
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Residues in contact with SER 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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131A THR* 4.0 10.1 - - - -
134A THR* 2.9 27.1 + - - +
135A ALA* 3.0 30.6 + - - +
173A VAL 2.6 24.2 + - - -
174A TRP* 3.5 9.1 - - - -
175A VAL 3.2 0.2 - - - -
176A PHE* 1.3 75.6 - - - +
178A ILE* 1.3 60.6 + - - +
180A ILE* 2.8 24.8 - - - +
181A SER* 2.9 12.2 + - - -
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Residues in contact with ILE 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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131A THR* 5.5 4.7 - - - +
174A TRP* 2.8 89.0 + - + +
175A VAL* 2.7 28.3 - - + +
177A SER* 1.3 73.3 - - - +
179A SER* 1.3 64.1 + - - +
181A SER* 4.3 3.8 - - - +
182A LEU* 2.6 46.5 + - + +
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Residues in contact with SER 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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175A VAL 2.7 19.5 + - - -
176A PHE* 3.6 15.0 - - - -
177A SER 3.2 0.2 - - - -
178A ILE* 1.3 79.6 - - - +
180A ILE* 1.3 58.9 + - - +
183A PRO* 2.8 29.9 - - - +
208A TYR* 4.7 0.2 + - - -
211A TYR* 3.3 25.2 + - - -
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Residues in contact with ILE 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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130A ILE* 3.4 20.4 - - + +
133A CYS* 4.6 5.4 - - - -
134A THR* 2.9 33.2 - - - +
137A ILE* 5.7 0.7 - - + -
176A PHE 3.2 9.6 + - - +
177A SER 2.8 22.0 + - - +
179A SER* 1.3 82.9 - - - +
181A SER* 1.3 61.0 + - - +
183A PRO* 3.7 0.2 - - - +
184A PRO* 3.1 17.3 - - - +
208A TYR* 2.6 30.2 + - - +
211A TYR* 5.3 8.7 - - + -
212A SER* 5.3 0.7 - - - -
215A GLY 5.6 0.2 - - - -
216A ALA* 3.4 37.0 - - + +
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Residues in contact with SER 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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126A LEU* 5.2 2.4 - - - +
127A SER* 3.4 30.5 + - - -
130A ILE* 3.7 20.8 - - - +
131A THR* 4.2 13.5 - - - -
177A SER 2.9 13.7 + - - -
178A ILE* 4.2 2.9 - - - -
180A ILE* 1.3 79.5 - - - +
182A LEU* 1.3 60.3 + - - +
184A PRO* 2.9 22.5 - - - +
185A PHE* 4.3 7.7 - - - -
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Residues in contact with LEU 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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178A ILE* 2.6 33.2 + - + +
179A SER* 5.2 0.4 - - - -
181A SER* 1.3 71.3 - - - +
183A PRO* 1.3 76.1 - - + +
184A PRO 3.1 1.0 - - - -
185A PHE* 3.2 36.9 + - + +
186A PHE* 5.8 4.7 - - + +
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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
------------------------------------------------------------
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