Contacts of the strand formed by residues 144 - 154 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A SER* 6.4 0.2 - - - -
120A PHE* 3.5 12.6 - - + -
140B THR* 2.9 21.6 - - - -
141B SER* 3.1 15.7 + - - +
142B GLY 4.6 1.0 - - - +
143B GLY* 1.3 80.4 + - - +
145B ALA* 1.3 71.9 + - - +
192B THR* 4.0 17.9 - - + -
193B VAL 3.6 12.3 + - - +
194B PRO* 5.1 1.6 - - - +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 4.1 1.6 - - - -
135B PRO* 4.2 6.5 - - + -
139B SER 3.1 16.8 - - - +
140B THR* 3.5 8.5 - - - +
144B THR* 1.3 77.8 - - - +
146B ALA* 1.3 59.7 + - - +
191B VAL 4.1 0.2 - - - +
192B THR* 3.3 4.5 - - - -
193B VAL* 3.0 36.5 + - + +
195B SER* 3.9 11.3 - - - +
198B LEU* 3.9 29.6 - - + -
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 3.4 37.3 - - + -
122A PHE* 3.4 16.0 - - + -
139A LEU* 4.0 11.2 - - + -
135B PRO* 3.1 10.0 - - - +
139B SER* 2.7 28.8 + - - -
145B ALA* 1.3 74.8 - - - +
147B LEU* 1.3 62.1 + - - +
191B VAL 3.4 6.1 - - - +
192B THR* 4.0 7.9 - - + -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PHE* 4.1 6.1 - - - -
133B LEU* 3.5 9.2 - - - +
135B PRO* 3.5 20.6 - - + -
145B ALA 5.3 0.4 - - - +
146B ALA* 1.3 76.2 - - - +
148B GLY* 1.3 58.7 + - - +
163B TRP* 3.8 19.3 - - + -
190B VAL* 3.3 5.0 - - - +
191B VAL* 2.8 63.0 + - + +
193B VAL* 4.1 11.4 - - + -
198B LEU* 4.0 22.0 - - + -
203B TYR* 3.7 39.3 - - + -
220B ALA* 4.3 6.1 - - + +
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU* 2.7 45.4 + - - +
147B LEU* 1.3 80.3 - - - +
149B CYS* 1.3 62.1 + - - -
163B TRP* 3.5 14.1 - - - -
189B SER 3.0 14.1 - - - -
190B VAL* 4.0 1.1 - - - -
220B ALA* 3.6 6.8 - - - +
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Residues in contact with CYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B VAL* 4.3 7.6 - - + -
131B PHE 3.2 9.9 - - - +
132B PRO* 4.5 0.9 - - - -
133B LEU* 3.9 6.0 - - - +
148B GLY* 1.3 79.7 - - - -
150B LEU* 1.3 60.8 + - - +
151B VAL* 3.9 8.3 + - + +
161B VAL* 5.3 2.7 - - + -
163B TRP* 3.7 5.0 - - + -
188B SER* 3.3 2.6 - - - -
189B SER 2.9 32.0 + - - +
205B CYS* 2.0 51.1 - - + -
207B VAL* 5.1 0.2 - - + -
218B LYS* 4.0 19.3 - - - -
220B ALA* 5.0 2.0 - - - -
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLN* 4.4 2.0 - - - +
135A SER* 3.5 35.0 - - - +
137A VAL* 4.6 12.1 - - + -
182A THR* 4.7 10.5 - - + +
129B SER 3.6 1.0 - - - +
130B VAL* 3.3 6.1 - - - +
131B PHE* 2.8 51.8 + - + +
133B LEU* 4.1 12.6 - - + +
149B CYS* 1.3 72.6 - - - +
151B VAL* 1.3 61.6 + - - +
152B LYS* 4.3 17.0 - - + -
186B SER* 3.9 15.9 - - - +
187B LEU 3.7 12.3 - - - +
188B SER* 3.3 19.5 - - - +
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PRO* 3.6 23.8 - - + -
129B SER 3.6 3.1 - - - -
130B VAL* 4.4 2.2 - - + +
149B CYS* 4.1 11.2 - - + +
150B LEU* 1.3 75.2 - - - +
152B LYS* 1.3 58.5 + - - +
154B TYR* 3.9 11.3 - - + -
159B VAL* 4.2 11.7 - - + -
161B VAL* 4.3 7.9 - - + -
186B SER* 3.3 5.0 - - - -
187B LEU* 2.7 54.2 + - + +
189B SER 5.4 0.2 - - - +
207B VAL* 3.7 40.4 - - + -
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Residues in contact with LYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLN* 3.6 22.9 - - - +
133A THR* 5.2 4.7 - - - -
135A SER* 3.6 20.1 + - - +
184A THR* 4.8 15.0 + - - +
128B PRO* 3.1 8.1 - - - +
129B SER* 2.7 44.8 + - - +
131B PHE* 4.4 12.3 - - + -
150B LEU* 4.3 15.7 - - + -
151B VAL* 1.3 73.0 - - - +
153B ASP* 1.3 83.7 + - - +
154B TYR 3.8 0.7 - - - -
180B GLN* 2.5 31.3 + - - -
185B TYR 3.9 0.4 - - - -
186B SER* 3.7 12.0 + - - +
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Residues in contact with ASP 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LYS* 2.8 35.1 + - - +
127B GLY 3.1 6.2 - - - +
129B SER* 5.2 4.3 + - - +
152B LYS* 1.3 98.3 + - - +
154B TYR* 1.3 56.9 + - - +
180B GLN* 2.6 31.9 + - - +
182B SER* 4.5 2.1 + - - -
184B LEU* 3.7 22.4 - - + +
185B TYR 3.0 14.7 + - - -
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Residues in contact with TYR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LYS* 3.2 13.9 - - - +
128B PRO* 3.6 34.3 - - + -
151B VAL* 3.9 24.5 - - + -
153B ASP* 1.3 76.1 - - - +
155B PHE* 1.3 63.7 + - - +
156B PRO 3.5 20.4 - - - -
157B GLU* 2.8 29.7 + - - -
159B VAL* 4.3 10.8 - - + +
177B ALA* 3.2 16.3 - - - +
184B LEU* 3.7 4.7 - - - +
185B TYR* 2.9 59.2 + + + +
186B SER* 4.1 2.9 - - - -
187B LEU* 3.5 13.9 - - + +
209B HIS* 3.6 13.2 - + + -
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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