Contacts of the strand formed by residues 157 - 163 (chain A) in PDB entry 2QK9
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 ARG 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A CYS* 3.0 1.9 - - - -
149A SER* 2.6 49.2 + - - +
155A ARG* 4.0 9.0 - - + +
156A PRO* 1.3 79.1 - - - +
158A ALA* 1.3 61.2 + - - +
175A ARG* 3.3 12.7 - - - +
180A GLN* 3.8 3.6 - - - -
281A ALA* 2.9 33.3 + - + +
282A LYS* 3.5 12.3 + - - +
283A GLN 2.9 27.1 + - - -
1005A SO4 2.8 39.2 + - - -
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Residues in contact with ALA 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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147A CYS 3.0 11.4 - - - +
148A CYS* 3.8 16.2 - - + -
157A ARG* 1.3 74.9 - - - +
159A GLY* 1.3 58.8 - - - +
175A ARG* 3.2 13.6 + - - +
176A LEU* 2.9 45.4 + - + +
180A GLN* 3.0 18.6 + - - +
181A THR 4.2 4.0 - - - +
185A ALA* 4.1 4.0 - - + -
281A ALA* 3.9 4.5 - - - -
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Residues in contact with GLY 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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146A GLY* 3.2 4.2 - - - -
147A CYS* 2.7 40.3 + - - +
158A ALA* 1.3 76.0 - - - +
160A ILE* 1.3 65.2 + - - -
174A ILE 3.2 12.8 - - - -
176A LEU 4.0 1.8 - - - -
185A ALA* 3.6 2.5 - - - +
277A ALA* 3.6 19.6 - - - +
281A ALA 4.2 2.5 - - - -
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Residues in contact with ILE 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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145A ASP 3.4 4.3 - - - -
159A GLY* 1.3 77.6 - - - -
161A GLY* 1.3 58.9 + - - +
162A VAL* 5.7 0.4 - - + -
172A VAL* 3.8 2.0 - - + +
173A GLY* 3.4 3.5 - - - -
174A ILE* 3.0 56.9 + - + +
175A ARG 5.3 1.3 - - - +
176A LEU* 4.0 25.1 - - + -
177A PRO* 6.2 1.8 - - + -
185A ALA* 3.5 23.1 - - - +
188A HIS* 4.0 5.4 - - + +
189A ALA* 3.7 15.5 - - - +
192A LYS* 3.9 34.1 - - + -
277A ALA* 3.7 5.2 - - - -
1003A GOL 4.4 11.2 - - - +
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Residues in contact with GLY 161 (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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143A TYR 3.8 0.5 - - - +
144A THR* 3.2 5.5 - - - -
145A ASP 2.7 36.0 + - - -
160A ILE* 1.3 75.9 - - - +
162A VAL* 1.3 66.6 + - - +
163A TYR 4.2 0.2 - - - -
172A VAL 3.2 8.7 - - - -
189A ALA* 4.1 0.7 - - - +
273A ALA* 3.6 23.3 - - - +
276A LEU* 4.0 0.7 - - - -
277A ALA* 3.8 4.9 - - - +
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Residues in contact with VAL 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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142A VAL* 3.6 18.6 - - + -
143A TYR 3.5 2.7 - - - +
144A THR* 4.5 1.3 - - + -
160A ILE* 5.4 1.1 - - + -
161A GLY* 1.3 79.8 - - - +
163A TYR* 1.3 61.6 + - - +
164A TRP* 3.3 25.6 - - - +
171A ASN* 3.3 7.5 - - - -
172A VAL* 2.9 42.3 + - + +
189A ALA* 3.6 24.9 - - - +
192A LYS* 3.8 23.3 - - + -
193A ALA* 3.9 9.9 - - + +
196A GLN* 3.4 5.6 - - - +
276A LEU* 3.7 4.1 - - - +
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Residues in contact with TYR 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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142A VAL* 3.6 4.7 - - - +
143A TYR* 2.8 45.8 + + + +
162A VAL* 1.3 75.2 - - - +
164A TRP* 1.3 60.8 + - - +
165A GLY* 3.4 27.1 - - - -
166A PRO* 3.1 28.8 - - + +
167A GLY 5.2 0.2 - - - -
171A ASN* 3.5 17.5 - - - -
267A PHE* 5.7 1.1 - + - -
268A ILE* 3.9 20.6 - - + +
269A GLY* 3.7 30.7 - - - +
272A GLU* 3.4 35.7 - - + -
273A ALA* 4.2 16.4 - - - +
276A LEU* 4.5 2.7 - - + -
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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