Contacts of the helix formed by residues 161 - 180 (chain A) in PDB entry 1SIW
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 161 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A PRO* 3.5 10.7 - - - +
160A SER* 1.3 85.2 + - - +
162A TRP* 1.3 66.3 + - - +
163A GLN* 3.7 7.8 + - - +
164A GLU* 3.2 21.8 + - - +
165A VAL* 2.9 24.4 + - - +
818A GLU* 5.1 3.4 - - - -
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Residues in contact with TRP 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PRO* 3.6 8.5 - - + +
161A SER* 1.3 74.3 - - - +
163A GLN* 1.3 58.0 + - - +
165A VAL* 3.7 6.7 - - + -
166A ASN* 2.8 61.0 + - - +
786A LEU* 3.9 22.0 - - + -
787A PRO* 3.7 32.1 - - + -
818A GLU* 2.9 47.9 + - + +
820A LYS* 3.8 39.0 - - + +
825A ILE* 3.8 36.6 - - + -
828A ALA* 6.2 1.3 - - + -
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Residues in contact with GLN 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A SER* 3.2 7.7 + - - +
162A TRP* 1.3 81.0 - - - +
164A GLU* 1.3 60.9 + - - +
166A ASN* 4.2 4.2 - - - +
167A GLU* 3.4 23.6 + - + +
832A LYS* 5.3 7.2 - - - +
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A MET* 4.0 13.2 - - + -
118A MET* 4.4 4.3 - - - +
121A TRP* 3.7 19.3 + - - +
122A ARG* 2.6 55.7 + - - +
125A LYS* 5.8 0.3 - - - +
160A SER* 2.8 26.6 + - - +
161A SER* 3.2 16.0 + - - +
163A GLN* 1.3 82.2 - - - +
165A VAL* 1.3 61.2 + - - +
167A GLU* 3.6 5.1 + - - +
168A LEU* 3.3 20.4 + - - +
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Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PRO* 4.1 11.2 - - + -
112A MET 4.7 3.6 - - - +
113A MET* 3.9 16.8 - - + -
160A SER* 3.5 25.1 - - - +
161A SER 2.9 19.3 + - - +
162A TRP* 3.4 18.4 - - + +
164A GLU* 1.3 74.1 - - - +
166A ASN* 1.3 65.2 + - - +
168A LEU* 3.4 2.4 + - - +
169A ILE* 2.8 36.3 + - + +
784A ILE* 4.2 18.2 - - + -
786A LEU* 3.7 25.6 - - + -
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Residues in contact with ASN 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A TRP* 2.8 53.9 + - - +
163A GLN* 4.2 4.8 - - - +
165A VAL* 1.3 77.7 - - - +
167A GLU* 1.3 58.3 + - - +
169A ILE* 3.9 1.4 - - - +
170A ALA* 3.0 29.8 + - - +
786A LEU* 5.4 0.2 - - - +
820A LYS* 5.5 1.6 - - - +
825A ILE 4.8 1.2 - - - +
828A ALA* 4.2 22.7 + - - +
829A ILE* 3.0 32.2 + - + +
832A LYS* 3.6 19.9 - - + +
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Residues in contact with GLU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TRP* 3.8 4.6 + - + -
125A LYS* 2.6 44.8 + - - +
131A PRO* 3.7 30.9 - - + +
163A GLN* 3.4 16.9 + - + +
164A GLU* 3.9 5.7 - - - +
165A VAL 3.3 0.4 - - - -
166A ASN* 1.3 76.5 - - - +
168A LEU* 1.3 60.2 + - - +
170A ALA* 3.4 1.4 + - - +
171A ALA* 2.8 28.8 + - - +
832A LYS* 3.8 33.7 + - - +
836A VAL* 5.0 1.2 - - + +
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Residues in contact with LEU 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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113A MET* 3.9 25.6 - - + -
117A LEU* 4.3 12.3 - - + -
121A TRP* 3.7 52.8 - - + -
135A TRP* 4.0 21.7 - - + -
164A GLU 3.3 14.8 + - - +
165A VAL* 3.8 4.7 - - - +
167A GLU* 1.3 79.5 - - - +
169A ILE* 1.3 61.5 + - - +
171A ALA* 3.4 1.0 + - - +
172A SER* 2.9 21.3 + - - -
767A LEU* 4.1 22.4 - - + -
784A ILE* 4.2 10.1 - - + -
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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 VAL* 2.8 24.1 + - + +
166A ASN* 3.9 5.2 - - - +
168A LEU* 1.3 77.9 - - - +
170A ALA* 1.3 57.7 + - - +
172A SER* 3.8 3.3 - - - -
173A ASN* 2.9 39.7 + - - +
710A PHE* 3.5 36.3 - - + -
767A LEU* 3.6 7.4 - - + -
769A VAL* 3.3 26.9 - - + -
784A ILE* 3.2 36.6 - - + -
786A LEU* 5.4 2.0 - - + -
829A ILE* 4.2 21.5 - - + -
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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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166A ASN 3.0 19.8 + - - +
167A GLU 3.7 2.9 - - - +
169A ILE* 1.3 74.6 - - - +
171A ALA* 1.3 65.2 + - - +
173A ASN* 3.3 7.1 + - - +
174A VAL* 2.9 30.5 + - - +
205A TYR* 5.1 1.1 - - - -
829A ILE* 4.8 3.8 - - + +
832A LYS* 3.9 9.9 - - + -
833A PHE* 3.8 36.3 - - + +
836A VAL* 4.0 7.2 - - + -
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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
----------------------------------------------------------
121A TRP* 4.0 7.6 - - + -
131A PRO* 3.4 41.1 - - + +
132A VAL* 4.0 4.8 - - - +
135A TRP* 4.4 4.3 - - + -
167A GLU 2.8 21.7 + - - +
168A LEU 3.7 3.6 - - - +
170A ALA* 1.3 73.2 - - - +
172A SER* 1.3 62.7 + - - +
174A VAL* 3.1 4.3 + - - +
175A TYR* 2.9 25.4 + - - +
836A VAL* 4.0 10.9 - - - +
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Residues in contact with SER 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TRP* 3.3 40.9 + - - -
168A LEU* 2.9 23.5 + - - -
169A ILE* 3.8 3.6 - - - -
171A ALA* 1.3 76.0 - - - +
173A ASN* 1.3 61.6 + - - +
175A TYR* 3.5 1.4 + - - +
176A THR* 2.9 30.0 + - - -
708A ASN* 2.8 30.7 + - - -
767A LEU* 3.9 7.4 - - - +
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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
----------------------------------------------------------
169A ILE* 2.9 23.6 + - - +
170A ALA 3.6 4.3 - - - +
172A SER* 1.3 76.8 + - - +
174A VAL* 1.3 63.6 + - - +
176A THR* 3.3 2.6 + - - -
177A ILE* 2.9 34.8 + - + +
185A VAL* 4.2 10.0 - - - +
205A TYR* 2.7 31.5 + - - +
209A ILE* 6.0 1.1 - - + -
708A ASN* 3.0 29.2 + - - +
710A PHE* 3.4 28.9 - - - -
767A LEU* 5.8 1.8 - - - +
833A PHE* 4.1 7.6 - - + -
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 3.8 17.5 - - + -
170A ALA 2.9 20.8 + - - +
171A ALA 3.5 6.3 - - - +
173A ASN* 1.3 76.6 - - - +
175A TYR* 1.3 57.9 + - - +
177A ILE* 3.7 1.2 - - - +
178A LYS* 2.9 34.4 + - + +
833A PHE* 3.6 24.0 - - + -
836A VAL* 4.2 5.6 - - + -
837A CYS* 3.8 27.4 - - + +
840A HIS* 3.7 31.0 - - + -
841A LEU* 4.3 10.6 - - + +
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Residues in contact with TYR 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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132A VAL* 4.1 20.2 - - + -
135A TRP* 3.5 31.2 - + + -
136A ALA* 3.6 26.7 - - + -
139A ILE* 3.6 18.9 - - + +
140A GLU* 2.8 40.0 + - - +
171A ALA 2.9 11.0 + - - +
172A SER 3.8 0.4 - - - +
174A VAL* 1.3 77.2 - - - +
176A THR* 1.3 64.1 + - - +
178A LYS* 4.6 2.0 - - - -
179A ASN* 3.0 63.2 + - - +
180A TYR* 4.0 27.3 + + - -
707A ARG* 5.7 0.7 - - - -
766A ASP* 5.3 4.3 - - - -
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Residues in contact with THR 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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135A TRP* 4.9 1.0 + - - -
172A SER* 2.9 19.7 + - - -
173A ASN 3.7 3.6 - - - -
175A TYR* 1.3 81.7 - - - +
177A ILE* 1.3 61.9 + - - +
180A TYR* 2.9 29.5 + - + -
181A GLY 3.0 7.2 + - - +
184A ARG* 3.7 32.5 - - + +
185A VAL* 3.7 16.6 - - + -
707A ARG* 4.2 17.4 - - + +
708A ASN* 3.3 19.5 + - - -
766A ASP* 5.1 1.7 + - - -
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Residues in contact with ILE 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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173A ASN* 2.9 23.3 + - + +
174A VAL 3.7 2.9 - - - +
176A THR* 1.3 75.0 - - - +
178A LYS* 1.3 62.6 + - - +
181A GLY* 3.2 22.6 + - - -
182A PRO* 3.9 18.2 - - + -
185A VAL* 4.0 11.0 - - + -
209A ILE* 4.1 26.0 - - + +
664A ASN* 3.3 6.4 + - - -
666A LEU* 3.7 26.8 - - + +
833A PHE* 3.9 31.0 - - + -
841A LEU* 3.9 13.2 - - + -
892A TYR* 3.7 13.5 - - + +
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Residues in contact with LYS 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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132A VAL* 5.4 5.1 - - + +
174A VAL* 2.9 19.0 + - + +
175A TYR 4.0 2.2 - - - +
177A ILE* 1.3 79.2 - - - +
179A ASN* 1.3 72.1 + - - +
664A ASN* 2.9 15.8 + - - -
666A LEU* 5.3 0.9 - - - -
667A THR* 5.7 1.2 - - - +
839A GLY 5.0 1.6 + - - -
840A HIS* 3.2 54.0 + - + +
841A LEU* 4.2 17.3 - - + -
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Residues in contact with ASN 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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140A GLU* 5.5 1.3 - - - -
175A TYR* 3.0 59.5 + - - +
178A LYS* 1.3 91.6 - - - +
180A TYR* 1.3 82.0 + - + +
664A ASN* 3.6 5.4 + - - +
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Residues in contact with TYR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 4.0 22.7 + + - -
176A THR* 2.9 15.5 + - - +
179A ASN* 1.3 98.1 - - + +
181A GLY* 1.3 61.3 + - - +
184A ARG* 3.6 36.7 + - + +
664A ASN* 3.2 27.0 + - - -
702A GLY 3.7 7.2 - - - -
703A LYS* 4.0 30.7 - - + +
707A ARG* 3.1 57.2 + - - -
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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
------------------------------------------------------------
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