Contacts of the strand formed by residues 149 - 154 (chain L) 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 LYS 149 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140L LEU* 4.6 1.9 - - - +
147L GLU* 2.6 39.3 + - - +
148L ALA* 1.3 84.1 + - - +
150L VAL* 1.3 62.0 + - - +
151L GLN* 5.5 7.4 - - + -
199L GLU 3.9 0.8 - - - +
200L VAL* 3.5 5.0 - - - +
201L THR* 2.9 50.4 + - - +
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Residues in contact with VAL 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138L CYS* 4.3 0.9 - - - -
140L LEU* 4.4 4.5 - - + -
149L LYS* 1.3 77.4 - - - +
151L GLN* 1.3 76.2 + - - +
152L TRP* 5.0 2.4 - - - +
165L GLU* 4.1 13.1 - - + +
179L LEU* 3.9 25.6 - - + -
181L SER* 3.9 29.0 + - - +
198L CYS* 3.2 36.1 - - - -
199L GLU 3.4 6.7 - - - +
200L VAL* 4.1 9.2 - - + -
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Residues in contact with GLN 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149L LYS* 5.4 6.3 - - + -
150L VAL* 1.3 85.2 + - - +
152L TRP* 1.3 67.4 + - - +
153L LYS* 4.2 1.7 + - - +
158L LEU* 3.4 35.6 - - + +
159L GLN 5.1 4.8 + - - +
198L CYS* 3.7 3.8 - - - -
199L GLU* 3.1 35.7 + - + +
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Residues in contact with TRP 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L ILE* 3.5 26.5 - - + -
136L VAL* 3.6 36.8 - - + -
137L VAL 3.8 1.3 - - - -
138L CYS* 3.5 27.1 - - + -
150L VAL* 5.0 2.4 - - + +
151L GLN* 1.3 80.9 - - - +
153L LYS* 1.3 65.5 + - - +
158L LEU* 3.3 7.3 - - - +
159L GLN* 2.8 48.9 + - + +
163L SER* 3.8 22.6 - - - -
165L GLU* 5.1 0.2 - - - -
181L SER* 2.9 46.9 + - - -
183L LEU* 3.7 28.5 - - + +
196L TYR* 5.1 1.6 - - + -
197L ALA 3.3 26.7 - - - -
198L CYS* 4.2 3.1 - - + -
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Residues in contact with LYS 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151L GLN 5.0 3.6 - - - +
152L TRP* 1.3 79.4 - - - +
154L VAL* 1.3 64.8 + - - +
155L ASP 4.1 0.4 + - - -
156L ASN* 3.3 47.0 + - - +
157L ALA 3.5 3.6 - - - -
158L LEU* 3.8 27.7 - - + +
195L VAL* 3.7 3.3 - - - +
197L ALA* 3.0 44.3 + - + +
199L GLU* 4.2 22.0 + - + +
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Residues in contact with VAL 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L TRP* 5.8 0.2 - - + -
153L LYS* 1.3 75.5 - - - +
155L ASP* 1.3 73.6 + - - +
157L ALA* 3.1 23.8 + - - +
159L GLN* 3.7 31.7 + - + +
183L LEU* 4.1 12.3 - - + -
185L LEU* 4.8 4.3 - - + -
193L HIS* 3.5 42.6 + - + +
195L VAL 3.5 3.1 - - - +
196L TYR* 3.7 33.4 - - + -
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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