Contacts of the strand formed by residues 156 - 164 (chain A) in PDB entry 3QK2
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 LEU 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A SER* 4.4 7.6 - - - +
154A ARG* 5.6 6.7 - - + +
155A THR* 1.3 81.9 - - - +
157A ALA* 1.3 62.7 + - - +
158A CYS 3.7 3.1 - - - +
159A PHE* 3.3 18.5 - - + -
202A ARG* 3.1 8.5 - - - +
203A HIS 2.8 28.4 + - - +
205A VAL* 4.5 8.3 - - + -
225A GLY* 3.7 29.4 - - - -
226A VAL 4.0 14.8 - - - +
227A ASN* 4.2 20.2 - - - +
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Residues in contact with ALA 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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156A LEU* 1.3 77.2 - - - +
158A CYS* 1.3 59.9 + - - +
159A PHE* 3.9 3.4 - - - -
198A LEU* 3.2 10.2 - - + +
199A THR* 2.9 51.6 + - - +
200A PRO 5.7 0.2 - - - -
201A HIS 4.1 5.8 - - - +
202A ARG* 4.3 11.2 - - + +
229A GLU* 6.0 0.2 - - - -
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Residues in contact with CYS 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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156A LEU* 3.7 4.7 - - - +
157A ALA* 1.3 81.6 - - - +
159A PHE* 1.3 70.5 + - - +
196A PHE* 3.4 38.8 - - - -
197A PHE 3.3 9.2 - - - -
198A LEU* 3.6 7.6 - - + -
225A GLY* 3.7 1.0 - - - -
226A VAL* 2.9 41.1 + - - +
229A GLU* 3.5 31.2 - - + +
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Residues in contact with PHE 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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156A LEU* 3.3 33.2 - - + -
157A ALA 3.9 4.0 - - - -
158A CYS* 1.3 86.2 - - - +
160A ALA* 1.3 62.6 + - - +
196A PHE* 3.6 3.1 - - - -
197A PHE* 2.9 66.7 + + + +
199A THR* 3.9 14.8 - - + -
203A HIS* 3.5 23.6 - - + -
205A VAL* 3.8 28.0 - - + -
208A ILE* 3.8 25.4 - - + -
223A CYS* 5.1 2.0 - - - -
224A LYS 3.5 8.1 - - - +
225A GLY* 4.0 11.0 - - - -
226A VAL* 3.6 7.9 - - - +
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Residues in contact with ALA 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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138A PHE* 3.6 25.9 - - + -
146A LEU* 4.6 1.3 - - + -
159A PHE* 1.3 74.9 - - - +
161A ILE* 1.3 68.6 + - - +
194A ILE* 4.4 0.7 - - + -
195A LEU 3.0 13.7 - - - +
196A PHE* 4.7 3.4 - - + -
197A PHE* 4.7 0.7 - - - -
223A CYS* 3.5 1.4 - - - -
224A LYS 3.0 32.2 + - - +
226A VAL* 3.7 8.5 - - + +
232A MET* 3.7 20.0 - - + -
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Residues in contact with ILE 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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138A PHE* 3.8 2.2 - - - -
160A ALA* 1.3 79.2 - - - +
162A TYR* 1.3 61.7 + - - +
163A THR* 4.0 9.8 + - + +
171A LEU* 4.0 17.9 - - + -
175A ILE* 4.2 12.8 - - + -
193A ASN 3.9 0.5 - - - +
194A ILE* 3.2 5.5 - - - +
195A LEU* 2.8 41.5 + - + +
197A PHE* 3.8 26.7 - - + -
208A ILE* 4.7 0.9 - - + -
212A ALA* 4.0 24.0 - - + -
221A LEU* 3.7 27.1 - - + -
222A ILE 3.2 4.5 - - - +
223A CYS* 4.0 17.5 - - + -
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Residues in contact with TYR 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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135A PRO* 3.5 24.7 - - + +
137A ASP 3.3 29.4 - - - -
138A PHE* 3.6 28.9 - - + -
139A PRO* 3.8 21.9 - - + +
161A ILE* 1.3 72.7 - - - +
163A THR* 1.3 63.0 + - - +
189A SER* 3.9 17.9 + - - -
190A TYR* 6.2 0.2 - - - -
192A HIS* 3.6 35.2 - + + -
193A ASN 3.5 13.7 - - - -
194A ILE* 3.5 11.2 - - + -
220A PHE* 3.3 15.9 - + - -
222A ILE* 2.7 41.2 + - + -
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Residues in contact with THR 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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161A ILE* 4.2 13.7 - - + +
162A TYR* 1.3 77.1 - - - +
164A THR* 1.3 73.6 + - - +
167A LYS* 3.5 19.8 - - + -
168A ALA* 3.6 26.0 - - + +
171A LEU* 4.5 4.3 - - + -
192A HIS* 3.3 6.8 - - - +
193A ASN 3.0 30.5 + - - +
195A LEU* 5.7 0.4 - - + -
220A PHE* 2.7 35.8 + - - -
221A LEU* 3.9 9.8 - - - +
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Residues in contact with THR 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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163A THR* 1.3 83.7 + - - +
165A LYS* 1.3 60.3 + - - +
166A GLU* 3.6 14.1 + - - +
167A LYS* 3.2 27.2 + - - +
168A ALA* 2.9 28.2 + - - +
192A HIS* 4.0 16.4 - - + +
193A ASN 4.2 0.4 - - - -
218A PHE* 5.6 0.5 - - - -
219A SER* 3.9 26.1 - - - +
220A PHE* 3.9 17.9 - - + -
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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