Contacts of the strand formed by residues 156 - 163 (chain H) in PDB entry 3KCG
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 GLN 156 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16H VAL* 3.7 24.8 - - + +
19H GLY* 3.8 6.6 + - - +
20H GLU* 3.2 24.0 + - - +
21H ASP* 2.8 27.9 + - - +
139H SER* 3.1 7.3 - - - -
140H GLY 2.9 36.3 + - - +
144H VAL* 4.3 13.6 - - + +
152H ALA* 3.8 18.9 - - + +
154H VAL* 3.0 24.4 + - - +
155H LEU* 1.3 79.0 + - - +
157H TYR* 1.3 61.0 + - - +
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Residues in contact with TYR 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H VAL* 4.4 2.0 - - - -
19H GLY* 3.3 3.7 - - - -
20H GLU* 3.0 51.1 + - + +
21H ASP 3.5 19.3 - - - -
22H ALA* 3.7 13.5 - - - -
26H GLN* 3.7 25.0 + - - -
27H PHE* 3.5 32.5 - + + -
137H TYR* 4.4 25.6 - + + -
138H VAL 3.2 11.7 - - - +
139H SER* 4.1 2.5 - - - -
156H GLN* 1.3 74.6 - - - +
158H LEU* 1.3 66.4 - - - +
159H ARG* 5.5 0.9 - - + -
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Residues in contact with LEU 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H VAL* 3.7 12.6 - - + -
17H VAL 4.1 3.6 - - - +
18H GLY 3.9 9.9 - - - +
19H GLY* 4.3 2.2 - - - -
137H TYR* 3.4 5.7 - - - -
138H VAL* 2.9 38.4 + - + +
157H TYR* 1.3 80.2 - - - +
159H ARG* 1.3 77.9 + - - +
160H VAL* 3.6 19.2 + - + -
184H PHE* 4.5 1.1 - - + +
188H ARG* 3.7 33.9 - - + +
189H ASP* 3.3 40.2 - - - +
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Residues in contact with ARG 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H SER* 2.8 39.6 + - - +
136H GLY* 3.3 8.9 + - - +
137H TYR* 3.3 46.8 + - + -
157H TYR* 5.0 1.4 - - + -
158H LEU* 1.3 77.5 - - + +
160H VAL* 1.3 62.4 + - - +
161H PRO* 4.2 0.6 - - + +
184H PHE* 3.4 22.0 + - - -
188H ARG* 5.4 0.5 + - - -
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Residues in contact with VAL 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H SER* 3.7 2.0 - - - -
136H GLY 2.8 39.0 + - - +
138H VAL* 3.9 29.4 - - + -
158H LEU* 3.7 25.6 - - + +
159H ARG* 1.3 80.9 - - - +
161H PRO* 1.3 67.3 - - + +
183H ALA* 4.0 16.8 - - + +
184H GLY* 4.2 22.2 - - + +
189H ASP* 5.2 4.3 - - - +
199H HIS* 4.0 9.8 + - + -
228H TYR* 4.6 7.2 - - - +
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Residues in contact with PRO 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H GLY 3.4 11.0 - - - +
135H SER* 4.6 2.2 - - - -
159H ARG* 4.2 0.7 - - + +
160H VAL* 1.3 86.2 - - + +
162H LEU* 1.3 68.4 + - - +
163H VAL* 3.6 0.6 + - + -
183H ALA* 3.2 4.3 - - - -
184H GLY* 3.0 74.1 + - + +
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Residues in contact with LEU 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H LEU* 3.6 33.2 - - + +
132H LYS* 4.0 33.0 - - + +
134H GLY* 3.0 25.6 + - - +
160H VAL 3.9 0.6 + - - -
161H PRO* 1.3 78.2 - - - +
163H VAL* 1.3 66.8 + - - +
164H ASP* 4.2 1.1 + - - -
181H PHE* 3.7 26.2 - - + -
182H CYS 3.5 17.3 - - - +
183H ALA* 4.4 2.2 - - - -
199H HIS* 6.0 1.1 - - + +
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Residues in contact with VAL 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H PRO* 3.9 0.7 - - + +
162H LEU* 1.3 85.0 - - - +
164H ASP* 1.3 76.4 + - - +
165H ARG* 3.5 1.9 + - - -
167H THR* 4.0 23.1 - - + -
168H CYS* 4.4 4.0 - - + +
182H CYS* 2.9 30.6 + - + +
183H ALA* 4.0 2.0 - - - -
184H GLY 3.7 23.8 - - - +
185H HIS* 4.2 11.7 - - + +
225H TYR* 3.6 39.7 - - + -
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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