Contacts of the strand formed by residues 129 - 133 (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 SER 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LYS* 5.1 3.9 + - - +
127B GLY 3.9 1.0 + - - -
128B PRO* 1.3 72.5 - - - +
130B VAL* 1.3 60.8 + - - +
131B PHE* 3.5 30.8 - - - -
150B LEU 3.6 1.4 - - - +
151B VAL* 3.6 1.6 - - - -
152B LYS* 2.7 40.7 + - - +
153B ASP* 4.7 3.1 + - - +
13H GLN* 5.8 3.8 - - - +
122H SER 4.7 10.2 + - - -
123H ALA* 5.9 0.2 - - - -
124H SER* 4.5 9.3 + - - -
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Residues in contact with VAL 130 (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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127A GLU* 4.3 3.0 + - - +
128B PRO* 4.1 8.0 + - + +
129B SER* 1.3 79.8 - - - +
131B PHE* 1.3 70.8 + - - +
149B CYS* 4.3 2.9 - - + -
150B LEU 3.3 7.0 - - - +
151B VAL* 4.4 6.7 - - + -
205B CYS* 4.2 6.1 - - - -
207B VAL* 3.8 39.7 - - + -
216B VAL* 3.4 38.9 - - + +
218B LYS* 3.3 38.3 + - + -
13H GLN* 5.7 3.0 - - - +
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Residues in contact with PHE 131 (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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125A SER* 3.6 24.0 - - - +
127A GLU* 3.7 24.7 - - + -
128A GLN* 3.4 55.0 - - + +
131A SER* 4.6 7.0 - - - -
129B SER* 3.5 33.7 - - - -
130B VAL* 1.3 80.4 - - - +
132B PRO* 1.3 67.1 - - - +
133B LEU* 6.2 0.2 - - + -
149B CYS* 3.2 4.6 - - - -
150B LEU* 2.8 57.0 + - + +
152B LYS* 4.4 10.3 - - + -
218B LYS* 4.2 3.6 - - - -
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Residues in contact with PRO 132 (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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123A PRO 4.9 3.1 - - - +
125A SER* 3.8 29.2 + - - -
127A GLU* 4.9 2.9 - - + +
131B PHE* 1.3 89.3 - - + +
133B LEU* 1.3 67.0 + - - +
134B ALA* 3.8 8.5 + - + +
148B GLY 3.8 5.2 - - - +
149B CYS* 4.5 1.1 - - - -
218B LYS* 3.7 25.1 - - + -
219B LYS 3.6 23.3 - - - +
220B ALA* 4.4 7.4 - - - -
221B GLU 5.6 0.2 - - - +
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Residues in contact with LEU 133 (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* 3.8 34.1 - - + +
123A PRO 5.1 4.9 - - - +
135A SER 5.9 1.6 - - - +
137A VAL* 3.8 26.2 - - + -
131B PHE* 6.2 0.2 - - + -
132B PRO* 1.3 75.6 - - - +
134B ALA* 1.3 62.4 + - - +
135B PRO* 3.6 1.9 - - - +
147B LEU* 3.5 6.2 - - - +
148B GLY* 2.7 41.6 + - - +
149B CYS 3.9 16.4 - - - +
150B LEU* 4.1 15.3 - - + +
188B SER* 3.6 27.6 - - - +
190B VAL* 4.3 11.4 - - + -
220B ALA* 3.9 3.3 - - - +
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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