Contacts of the helix formed by residues 156 - 170 (chain A) in PDB entry 2XKL
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 PRO 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A SER 4.8 0.4 - - - +
131A PRO* 4.4 25.6 - - + +
154A HIS 4.6 0.2 - - - +
155A PRO* 1.3 87.2 - - + +
157A GLU* 1.3 53.9 + - + +
158A LYS* 3.0 33.4 - - + +
159A CYS* 2.8 35.8 + - + +
160A VAL* 4.2 0.7 + - - +
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Residues in contact with GLU 157 (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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155A PRO 3.3 5.8 + - - -
156A PRO* 1.3 69.6 - - + +
158A LYS* 1.3 63.3 + - + +
159A CYS 3.0 1.7 + - - -
160A VAL* 3.3 12.0 + - - +
161A GLU* 3.1 41.6 + - + +
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Residues in contact with LYS 158 (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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128A SER* 3.7 17.9 + - - -
129A SER* 3.3 32.6 + - - +
131A PRO* 4.8 3.4 - - - +
156A PRO* 2.8 26.9 + - + +
157A GLU* 1.3 79.1 - - + +
159A CYS* 1.3 60.5 + - - +
161A GLU* 3.9 19.4 - - + +
162A GLU* 3.1 31.6 + - - +
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Residues in contact with CYS 159 (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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129A SER* 3.3 13.2 + - - +
130A CYS* 2.0 53.9 - - + -
148A LEU* 3.9 20.0 - - - -
150A ASN* 4.6 10.5 - - - -
155A PRO* 4.6 13.9 - - + -
156A PRO* 2.8 16.4 + - + +
158A LYS* 1.3 77.4 - - - +
160A VAL* 1.3 67.5 + - - +
162A GLU* 3.2 2.4 + - - -
163A PHE* 2.9 24.4 + - - +
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Residues in contact with VAL 160 (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 ILE* 3.4 33.2 - - + -
51A ALA* 4.7 1.1 - - + -
148A LEU* 4.4 10.1 - - + -
155A PRO* 5.5 2.5 - - + -
156A PRO 4.2 0.6 + - - +
157A GLU* 3.3 13.0 + - - +
159A CYS* 1.3 79.9 - - + +
161A GLU* 1.3 61.1 + - + +
163A PHE* 3.4 1.4 + - - +
164A GLN* 2.8 31.7 + - + +
175A PHE* 3.9 11.0 - - + -
177A VAL* 3.7 37.7 - - + -
180A ARG* 4.5 4.3 - - - +
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Residues in contact with GLU 161 (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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157A GLU* 3.1 37.7 + - - +
158A LYS* 4.0 16.7 - - + +
159A CYS 3.2 0.2 - - - -
160A VAL* 1.3 78.5 - - + +
162A GLU* 1.3 59.6 + - - +
164A GLN* 3.2 12.6 + - - +
165A SER* 2.8 31.9 + - - -
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Residues in contact with GLU 162 (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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124A ASP* 5.4 5.6 - - - +
125A LEU* 3.6 21.2 - - + +
129A SER* 3.4 23.5 + - - +
158A LYS* 3.1 23.0 + - - +
159A CYS 3.2 1.1 + - - +
161A GLU* 1.3 78.3 - - - +
163A PHE* 1.3 57.7 + - - +
165A SER* 3.8 15.2 + - - -
166A LEU* 3.0 32.7 + - + +
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Residues in contact with PHE 163 (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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51A ALA* 3.9 14.4 - - + -
52A GLY 4.0 3.4 - - - -
53A ALA* 4.0 8.3 - - + -
125A LEU* 3.9 13.4 - - + +
135A MET* 3.6 33.0 - - + -
146A PHE* 3.6 30.5 - - + -
148A LEU* 3.7 47.6 - - + -
159A CYS 2.9 17.5 + - - +
160A VAL 3.8 2.0 - - - +
162A GLU* 1.3 73.0 - - - +
164A GLN* 1.3 53.9 + - - +
166A LEU* 4.0 3.5 - - + +
167A THR* 2.7 49.4 + - + +
175A PHE* 3.5 36.3 - + - -
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Residues in contact with GLN 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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160A VAL* 2.8 20.7 + - - +
161A GLU* 3.5 12.0 - - - +
163A PHE* 1.3 73.6 - - - +
165A SER* 1.3 59.5 + - - +
167A THR* 3.7 0.4 - - - -
168A SER* 2.8 40.1 + - - -
175A PHE* 3.5 39.8 - - + +
177A VAL* 5.9 0.2 - - - +
1192A EDO 3.0 31.2 + - - -
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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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161A GLU 2.8 17.8 + - - -
162A GLU* 3.8 19.2 + - - -
164A GLN* 1.3 79.2 - - - +
166A LEU* 1.3 58.1 + - - +
168A SER* 3.8 3.6 - - - -
169A CYS* 3.0 29.3 + - - +
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Residues in contact with LEU 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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124A ASP* 6.0 2.2 - - - +
125A LEU* 4.0 32.5 - - + -
135A MET* 4.1 17.9 - - + -
162A GLU* 3.0 19.4 + - + +
163A PHE* 4.0 6.7 - - + +
165A SER* 1.3 75.3 + - - +
167A THR* 1.3 68.4 + - + +
169A CYS* 3.3 20.1 + - + +
170A LEU* 3.5 20.6 + - + +
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Residues in contact with THR 167 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ALA* 3.4 28.9 - - + +
135A MET* 5.2 1.6 - - - -
146A PHE* 4.3 16.6 - - + -
163A PHE* 2.7 43.9 + - + +
164A GLN* 3.2 3.3 + - - -
166A LEU* 1.3 79.6 - - + +
168A SER* 1.3 63.7 + - - +
170A LEU* 3.2 8.5 + - - -
172A PHE* 3.0 33.0 + - - +
1192A EDO 2.7 20.8 + - - -
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Residues in contact with SER 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 GLN* 2.8 26.0 + - - -
165A SER* 3.8 5.2 - - - -
167A THR* 1.3 72.5 - - - +
169A CYS* 1.3 63.3 + - - +
171A ASP* 3.0 8.1 + - - -
172A PHE 4.0 4.7 - - - -
173A LYS* 2.7 39.3 + - - +
1192A EDO 3.1 28.0 + - - -
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Residues in contact with CYS 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 3.0 15.2 + - - +
166A LEU* 3.3 15.0 - - + +
167A THR 3.2 0.2 - - - -
168A SER* 1.3 77.3 - - - +
170A LEU* 1.3 72.4 + - + +
171A ASP* 3.4 3.1 + - - +
173A LYS* 5.3 0.2 + - - -
1193A NA 2.4 33.2 - - - -
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Residues in contact with LEU 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 LEU* 3.5 18.6 + - + +
167A THR* 3.2 3.7 + - - +
168A SER 3.2 1.0 - - - -
169A CYS* 1.3 96.6 - - + +
171A ASP* 1.3 66.4 - - - +
172A PHE* 3.4 31.6 - - + -
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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