Contacts of the helix formed by residues 163 - 178 (chain A) in PDB entry 2IGT
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A ASP* 2.9 6.7 + - - -
162A ALA* 1.3 77.1 - - - +
164A LYS* 1.3 62.9 + - - +
165A LYS* 3.4 6.8 + - - +
166A ALA* 3.0 22.7 + - - +
167A ILE* 3.0 24.9 + - - +
188A CYS* 4.0 2.0 - - - -
1001A SAM 3.4 20.8 + - - -
1008A ACY 2.6 28.7 + - - -
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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
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162A ALA 3.7 4.9 + - - -
163A SER* 1.3 71.5 - - - +
165A LYS* 1.3 58.2 + - - +
167A ILE* 3.3 4.8 + - - +
168A GLY 2.9 24.6 + - - -
188A CYS* 3.7 20.3 - - + -
1008A ACY 3.3 12.3 + - + +
1009A ACY 3.3 40.8 + - + +
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Residues in contact with LYS 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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105A THR* 6.1 0.4 - - - -
107A PHE* 6.4 1.8 - - - -
163A SER* 3.6 4.8 + - - +
164A LYS* 1.3 77.4 - - - +
166A ALA* 1.3 61.1 + - - +
168A GLY* 3.2 3.8 + - - -
169A TRP* 3.0 65.8 + - + +
1008A ACY 2.9 28.6 + - - +
1009A ACY 5.6 0.7 - - - -
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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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142A TYR* 3.7 11.9 - - - +
161A ASP* 3.7 17.0 - - - +
163A SER* 3.0 27.1 + - - +
165A LYS* 1.3 73.1 - - - +
167A ILE* 1.3 66.8 + - - +
169A TRP* 3.2 26.1 + - + +
170A ALA* 2.9 23.2 + - - +
1001A SAM 3.9 10.5 - - - +
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Residues in contact with ILE 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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159A HIS* 3.6 30.7 - - + +
161A ASP* 3.8 16.2 - - + +
163A SER 3.0 19.0 + - - +
164A LYS* 3.6 7.9 - - - +
166A ALA* 1.3 74.3 - - - +
168A GLY* 1.3 58.6 + - - +
170A ALA* 3.2 6.1 + - - +
171A LYS* 2.9 54.9 + - + +
186A TRP* 4.1 14.6 - - + -
187A ILE 3.7 21.8 - - - +
188A CYS* 4.2 14.8 - - + -
1009A ACY 3.7 10.3 - - - +
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Residues in contact with GLY 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 2.9 11.5 + - - -
165A LYS* 3.6 4.5 - - - -
166A ALA 3.2 0.2 - - - -
167A ILE* 1.3 76.7 - - - +
169A TRP* 1.3 57.4 + - - +
171A LYS* 3.4 4.6 + - - +
172A GLU* 3.0 34.9 + - - +
1009A ACY 3.6 26.0 - - - +
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Residues in contact with TRP 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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89A GLU* 4.9 1.6 + - - -
103A ARG* 3.4 44.1 + - - +
105A THR* 4.0 28.0 - - + -
109A HIS* 4.2 18.4 - + - -
111A GLY* 6.3 0.7 - - - -
142A TYR* 4.4 12.1 - + - -
143A THR* 4.0 26.0 - - + -
165A LYS* 3.0 57.6 + - + +
166A ALA* 3.2 24.7 + - + +
168A GLY* 1.3 72.8 - - - +
170A ALA* 1.3 66.4 + - - +
172A GLU* 3.3 15.0 + - - +
173A ASN* 3.0 27.5 + - - +
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Residues in contact with ALA 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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142A TYR 3.8 5.8 - - - +
143A THR* 3.4 30.4 + - - +
144A GLY* 4.4 0.2 - - - -
148A LEU* 4.6 1.4 - - - +
159A HIS* 4.0 2.9 - - + +
166A ALA 2.9 12.5 + - - +
167A ILE 3.6 6.7 - - - +
169A TRP* 1.3 77.0 - - - +
171A LYS* 1.3 57.7 + - - +
173A ASN* 3.1 5.0 + - - +
174A GLN* 2.8 27.0 + - - +
186A TRP* 3.3 31.8 - - + -
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Residues in contact with LYS 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 ILE* 2.9 30.3 + - - +
168A GLY* 3.6 5.2 - - - +
170A ALA* 1.3 73.2 - - - +
172A GLU* 1.3 65.1 + - - +
174A GLN* 3.2 12.1 + - - +
175A VAL* 3.0 29.6 + - + +
186A TRP* 3.6 40.2 - - + +
1009A ACY 2.8 36.3 + - - +
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Residues in contact with GLU 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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90A THR* 5.4 0.3 - - - +
101A LEU* 3.6 18.3 - - + +
103A ARG* 3.1 33.3 + - - +
168A GLY 3.0 19.4 + - - +
169A TRP* 3.4 16.1 - - - +
171A LYS* 1.3 75.1 - - - +
173A ASN* 1.3 57.0 + - - +
175A VAL* 3.4 9.7 + - - +
176A LEU* 3.1 27.4 + - - +
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Residues in contact with ASN 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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99A GLU 3.4 2.9 - - - +
100A PHE* 3.4 20.6 - - + +
101A LEU* 2.9 37.4 + - - +
103A ARG* 5.4 0.9 + - - -
143A THR* 3.0 36.3 + - - +
145A VAL* 4.9 1.6 - - - +
148A LEU* 3.6 17.7 - - + -
169A TRP* 3.0 16.4 + - - +
170A ALA 3.1 7.8 + - - +
172A GLU* 1.3 73.6 - - - +
174A GLN* 1.3 60.2 + - - +
176A LEU* 3.2 5.8 + - - -
177A ALA* 2.8 32.2 + - - +
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Residues in contact with GLN 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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148A LEU* 3.7 21.4 - - + +
170A ALA 2.8 16.6 + - - +
171A LYS* 3.2 12.3 + - - +
173A ASN* 1.3 73.1 - - - +
175A VAL* 1.3 61.4 + - - +
177A ALA* 3.3 1.1 + - - -
178A GLY 3.2 3.5 + - - -
179A LEU* 2.9 61.2 + - + +
180A GLU* 3.7 20.6 + - + +
182A ALA 4.1 7.5 + - - -
184A ILE* 3.9 14.7 + - + +
186A TRP* 3.1 33.8 + - + +
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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 LYS* 3.0 21.1 + - + +
172A GLU* 3.6 9.6 - - - +
173A ASN 3.2 0.2 - - - -
174A GLN* 1.3 75.3 - - + +
176A LEU* 1.3 67.0 + - + +
178A GLY* 3.0 14.9 + - - -
180A GLU* 3.7 41.0 - - + +
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Residues in contact with LEU 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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92A PRO* 4.9 11.0 - - + -
93A LEU 5.2 0.2 - - - +
99A GLU* 3.9 15.9 - - + +
100A PHE* 3.6 39.9 - - - +
101A LEU* 3.7 23.8 - - + -
172A GLU 3.1 16.8 + - - +
173A ASN* 3.7 4.9 - - - +
175A VAL* 1.3 78.6 - - + +
177A ALA* 1.3 60.7 + - - +
178A GLY* 3.4 0.9 + - - -
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Residues in contact with ALA 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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98A VAL* 4.3 4.3 - - + -
99A GLU* 3.3 36.4 + - - +
148A LEU* 4.3 7.6 - - + -
173A ASN 2.8 17.7 + - - +
174A GLN 3.9 3.8 - - - +
175A VAL 3.2 0.2 - - - -
176A LEU* 1.3 74.8 - - - +
178A GLY* 1.3 61.5 + - - +
179A LEU* 3.6 25.8 + - + +
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Residues in contact with GLY 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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175A VAL 3.0 14.3 + - - -
176A LEU 3.2 1.6 + - - -
177A ALA* 1.3 79.7 - - - +
179A LEU* 1.3 64.6 + - - +
180A GLU* 3.5 4.0 + - - -
181A GLN 5.3 0.5 + - - -
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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