Contacts of the strand formed by residues 144 - 154 (chain H) in PDB entry 3KDM
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 THR 144 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H SER* 2.7 47.3 + - - -
143H GLY* 1.3 80.0 - - - +
145H ALA* 1.3 63.4 + - - +
192H THR* 3.3 36.6 - - + +
193H VAL 3.4 8.7 - - - +
195H SER* 3.6 3.8 + - - -
120L PHE* 4.1 5.5 - - + -
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Residues in contact with ALA 145 (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 PRO* 5.1 2.2 - - + -
139H SER 5.7 1.3 - - - -
140H THR* 6.3 1.3 - - - +
141H SER 5.3 1.6 - - - +
144H THR* 1.3 75.5 - - - +
146H ALA* 1.3 62.6 + - - +
192H THR* 3.0 5.5 - - - -
193H VAL* 2.4 51.6 + - + +
195H SER* 3.9 9.8 + - - +
198H LEU* 3.8 38.1 - - + -
120L PHE* 4.3 3.8 - - - -
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Residues in contact with ALA 146 (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 PRO* 3.4 13.7 - - - +
136H SER 4.5 1.0 + - - -
145H ALA* 1.3 76.3 - - - +
147H LEU* 1.3 66.3 + - - +
191H VAL 3.3 8.3 - - - +
192H THR* 4.1 3.4 - - + -
120L PHE* 3.7 44.0 - - + -
122L PHE* 3.3 17.7 - - + -
139L LEU* 3.8 18.2 - - + -
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Residues in contact with LEU 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H LEU 3.2 15.3 - - - +
135H PRO* 3.2 33.4 - - + -
146H ALA* 1.3 77.4 - - - +
148H GLY* 1.3 61.8 + - - +
163H TRP* 3.7 13.7 - - + -
190H VAL* 3.3 5.8 - - - +
191H VAL* 2.9 49.7 + - + +
193H VAL* 4.8 4.3 - - + -
198H LEU* 3.8 9.4 - - + -
203H TYR* 3.7 27.1 - - + -
220H ALA* 3.6 25.8 - - + +
122L PHE* 3.8 9.2 - - - -
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Residues in contact with GLY 148 (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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133H LEU* 2.8 37.2 + - - +
147H LEU* 1.3 78.0 - - - +
149H CYS* 1.3 71.2 + - - -
163H TRP* 3.5 10.8 - - - -
189H SER 3.0 14.1 - - - -
190H VAL* 4.0 1.3 - - - -
220H ALA* 3.5 7.6 - - - +
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Residues in contact with CYS 149 (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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130H VAL* 4.2 7.9 - - + -
131H PHE 3.3 9.6 - - - +
132H PRO* 4.7 2.9 - - - -
133H LEU* 3.9 5.8 - - - +
148H GLY* 1.3 80.2 - - - -
150H LEU* 1.3 60.1 + - - +
151H VAL* 4.0 7.6 + - + +
161H VAL* 5.5 0.2 - - + -
163H TRP* 3.8 5.6 - - + -
188H SER* 3.1 5.4 - - - -
189H SER* 2.9 34.4 + - - +
205H CYS* 2.0 53.6 - - + -
207H VAL* 5.1 0.7 - - + -
218H LYS* 4.1 14.4 - - - -
220H ALA* 4.9 1.8 - - - -
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Residues in contact with LEU 150 (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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129H SER 3.4 2.3 - - - +
130H VAL* 3.3 6.8 - - - +
131H PHE* 2.8 57.0 + - + +
133H LEU* 4.1 12.9 - - + +
149H CYS* 1.3 71.2 - - - +
151H VAL* 1.3 60.8 + - - +
152H LYS* 4.1 13.2 - - + -
186H SER* 3.7 17.3 - - - +
187H LEU 3.6 11.2 - - - +
188H SER* 3.5 18.8 - - - +
128L GLN* 4.3 2.0 - - - +
135L SER* 3.4 37.0 - - - +
137L VAL* 4.9 8.3 - - + -
182L THR* 5.2 8.1 - - + +
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Residues in contact with VAL 151 (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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128H PRO* 3.5 24.2 - - + -
129H SER 3.7 3.1 - - - -
130H VAL* 4.4 5.2 - - + +
149H CYS* 4.4 8.1 - - + +
150H LEU* 1.3 75.0 - - - +
152H LYS* 1.3 57.2 - - - +
154H TYR* 3.7 12.3 - - + -
159H VAL* 4.0 24.0 - - + -
161H VAL* 4.1 13.5 - - + -
186H SER* 3.3 4.9 - - - -
187H LEU* 2.7 44.9 + - + +
189H SER 5.4 0.4 - - - +
207H VAL* 3.9 30.3 - - + -
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Residues in contact with LYS 152 (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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128H PRO* 3.5 2.0 - - - +
129H SER* 3.0 37.7 + - - +
131H PHE* 4.6 7.6 - - + -
150H LEU* 4.1 13.5 - - + -
151H VAL* 1.3 72.3 - - - +
153H ASP* 1.3 96.2 + - - +
154H TYR 3.7 1.1 - - - -
180H GLN* 2.8 27.7 + - - +
186H SER* 3.4 16.2 - - - +
128L GLN* 4.0 13.9 - - - +
133L THR* 4.3 13.0 - - - +
135L SER* 3.7 24.7 - - - +
182L THR* 6.3 1.3 - - + -
184L THR* 4.6 16.3 + - - +
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Residues in contact with ASP 153 (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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126H LYS* 3.0 35.3 + - - +
127H GLY 3.3 4.2 - - - +
129H SER* 5.7 2.5 + - - +
152H LYS* 1.3 104.8 + - - +
154H TYR* 1.3 57.1 + - - +
180H GLN* 3.0 21.1 + - - -
182H SER* 4.6 2.1 + - - -
184H LEU* 3.7 26.7 - - + +
185H TYR 2.9 17.0 + - - -
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Residues in contact with TYR 154 (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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126H LYS 3.0 12.3 - - - +
128H PRO* 3.6 23.8 - - + -
151H VAL* 3.7 31.9 - - + -
153H ASP* 1.3 79.7 - - - +
155H PHE* 1.3 63.8 + - - +
156H PRO 3.4 19.7 - - - -
157H GLU* 2.9 29.8 + - - -
159H VAL* 3.5 32.7 - - + +
177H ALA* 3.2 16.8 - - - +
184H LEU* 3.8 2.4 - - - -
185H TYR* 2.9 55.0 + + + +
186H SER* 4.1 3.4 - - - -
187H LEU* 3.6 4.5 - - + +
209H HIS* 3.8 10.3 - + - +
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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