Contacts of the helix formed by residues 164 - 176 (chain A) in PDB entry 1ISR
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 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A TRP* 3.5 36.5 + - - -
162A PRO* 4.3 0.9 - - - +
163A GLY* 1.3 79.1 - - - +
165A SER* 1.3 67.5 + - - +
166A SER* 3.5 13.7 + - - -
167A VAL* 3.5 24.8 + - - +
168A ALA* 3.0 26.2 + - - +
187A ALA* 4.3 0.2 - - - +
236A TYR* 5.1 2.3 - - - +
292A GLU* 4.2 8.3 + - - -
1001A GLU 3.7 11.2 + - - -
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Residues in contact with SER 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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164A SER* 1.3 74.9 + - - +
166A SER* 1.3 59.6 + - - -
167A VAL 3.1 1.3 - - - -
168A ALA* 3.0 7.1 + - - +
169A ILE* 2.9 37.0 + - - +
187A ALA* 3.9 3.2 - - - -
188A THR 3.6 2.6 + - - -
189A SER* 3.4 37.0 + - - -
192A LEU* 4.6 3.8 - - - -
235A ASN* 4.3 5.2 - - - -
236A TYR* 4.1 10.9 - - - +
1001A GLU* 2.7 30.9 + - - -
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Residues in contact with SER 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 3.5 13.8 + - - -
164A SER* 3.5 7.9 + - - -
165A SER* 1.3 77.9 - - - +
167A VAL* 1.3 63.8 + - - +
169A ILE* 3.6 7.2 + - - +
170A GLN* 3.3 16.8 + - - +
234A GLY* 3.6 7.8 - - - -
235A ASN* 2.7 39.9 + - - -
236A TYR* 4.0 2.1 + - - +
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Residues in contact with VAL 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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108A SER* 5.1 2.2 - - - -
110A TRP* 4.3 7.0 - - + -
111A HIS* 4.0 17.7 - - - +
112A SER* 3.6 24.2 - - - +
115A ALA* 3.4 31.0 - - + -
162A PRO* 3.6 17.7 - - + -
164A SER* 3.5 30.2 + - - +
165A SER 3.1 0.2 - - - -
166A SER* 1.3 76.5 - - - +
168A ALA* 1.3 64.0 + - - +
170A GLN* 3.4 2.4 + - - +
171A VAL* 3.1 29.6 + - - +
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Residues in contact with ALA 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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161A GLY 5.5 0.2 - - - -
162A PRO* 3.7 17.5 - - + +
164A SER 3.0 18.7 + - - +
165A SER* 3.0 10.6 + - - +
167A VAL* 1.3 76.0 - - - +
169A ILE* 1.3 59.5 + - - +
171A VAL 3.4 0.3 + - - -
172A GLN* 2.8 32.4 + - - +
182A GLN* 3.5 15.3 + - - +
187A ALA* 4.1 15.9 - - + -
192A LEU* 4.4 9.6 - - + -
201A PHE* 4.7 3.1 - - + -
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Residues in contact with ILE 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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165A SER 2.9 20.3 + - - +
166A SER* 3.8 6.1 - - - +
168A ALA* 1.3 76.2 - - - +
170A GLN* 1.3 58.3 + - - +
172A GLN* 3.5 4.8 - - - +
173A ASN* 2.8 46.7 + - - +
191A ASP* 5.0 3.1 - - + -
192A LEU* 3.6 24.2 - - + -
198A TYR* 3.4 31.4 - - + +
235A ASN* 3.3 44.4 - - + +
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Residues in contact with GLN 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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112A SER* 3.7 38.4 + - - +
116A LEU* 4.0 33.0 - - + +
166A SER 3.3 10.6 + - - +
167A VAL 3.5 9.0 - - - +
168A ALA 3.2 0.4 - - - -
169A ILE* 1.3 78.6 - - - +
171A VAL* 1.3 64.9 + - + +
173A ASN* 3.0 28.6 + - - +
174A LEU* 3.5 7.6 + - - +
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Residues in contact with VAL 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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50A LEU* 4.0 19.1 - - + -
115A ALA* 4.2 15.9 - - + +
116A LEU* 5.2 2.0 - - - -
119A SER* 3.4 27.4 - - - +
122A PHE* 6.2 0.7 - - + -
159A VAL* 5.2 2.0 - - + -
162A PRO* 3.9 17.7 - - + -
167A VAL 3.1 17.6 + - - +
168A ALA 3.9 2.9 - - - +
170A GLN* 1.3 78.2 - - + +
172A GLN* 1.3 57.5 + - - +
174A LEU* 3.3 6.0 + - - +
175A LEU* 3.0 47.9 + - + +
182A GLN* 3.6 7.6 - - - +
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Residues in contact with GLN 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 ALA 2.8 19.7 + - - +
169A ILE* 3.5 8.1 - - - +
171A VAL* 1.3 73.8 - - - +
173A ASN* 1.3 60.9 + - - +
174A LEU 3.0 5.9 + - - -
175A LEU* 4.5 5.0 - - - +
176A GLN* 3.1 32.5 + - - +
182A GLN* 3.1 36.7 + - - +
192A LEU* 5.5 1.3 - - + -
198A TYR* 3.6 33.7 - - + -
200A TYR* 3.2 38.3 + - - +
201A PHE* 3.4 14.9 + - + +
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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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169A ILE* 2.8 30.6 + - - +
170A GLN* 3.0 20.1 + - - +
172A GLN* 1.3 75.1 - - - +
174A LEU* 1.3 57.3 + - - +
176A GLN* 3.9 17.6 + - - +
177A LEU* 3.7 19.2 - - - +
197A LEU 4.9 0.2 + - - -
198A TYR* 3.4 28.5 - - - -
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Residues in contact with LEU 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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116A LEU* 4.0 14.6 - - + -
119A SER* 3.7 33.2 - - - +
120A ILE* 3.7 29.2 - - + -
123A ILE* 4.5 8.1 - - + -
170A GLN 3.5 6.8 + - - +
171A VAL 3.3 8.0 + - - +
172A GLN 3.0 0.6 - - - -
173A ASN* 1.3 79.9 - - - +
175A LEU* 1.3 63.0 + - + +
176A GLN 3.2 1.6 - - - -
177A LEU* 2.9 41.2 + - + +
178A PHE* 3.7 19.4 - - + -
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Residues in contact with LEU 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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119A SER* 5.3 8.3 - - - +
122A PHE* 5.1 9.4 - - + -
123A ILE* 4.8 9.0 - - + -
159A VAL* 3.6 35.9 - - + -
171A VAL* 3.0 26.7 + - + +
172A GLN* 4.4 3.8 - - - +
174A LEU* 1.3 81.4 - - + +
176A GLN* 1.3 57.9 + - - +
177A LEU 3.0 0.2 - - - -
178A PHE* 3.0 21.4 + - - +
179A ASP 3.2 8.1 + - - -
180A ILE* 3.3 45.7 + - + +
182A GLN* 3.1 31.2 - - + +
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Residues in contact with GLN 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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172A GLN* 3.1 30.0 + - - +
173A ASN* 3.9 24.9 + - - +
175A LEU* 1.3 75.7 - - - +
177A LEU* 1.3 68.9 + - + +
178A PHE 3.2 1.0 + - - -
179A ASP* 3.6 15.2 + - - +
180A ILE 5.0 0.2 + - - -
197A LEU 2.8 32.0 + - - +
198A TYR* 4.0 8.3 - - - +
199A LYS* 4.1 7.1 - - - +
200A TYR* 4.3 24.2 - - + -
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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