Contacts of the strand formed by residues 133 - 143 (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 THR 133 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152H LYS* 4.3 12.1 - - - -
128L GLN* 3.1 41.0 - - - +
129L LEU* 3.8 7.2 - - - +
131L SER* 3.3 11.0 + - - -
132L GLY* 1.3 82.4 + - - +
134L ALA* 1.3 69.8 + - - +
184L THR* 4.1 17.9 - - + +
185L LEU 3.5 10.6 + - - +
186L SER* 5.0 1.6 - - - -
187L LYS* 3.9 1.7 - - - +
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Residues in contact with ALA 134 (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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124L PRO* 3.8 9.6 - - + -
128L GLN* 4.1 0.4 - - - -
129L LEU* 3.3 25.1 - - + -
133L THR* 1.3 76.4 - - - +
135L SER* 1.3 61.0 + - - +
136L VAL* 5.0 1.3 - - + +
183L LEU 3.5 1.2 - - - +
184L THR* 3.5 4.5 - - - -
185L LEU* 2.5 41.8 + - + +
186L SER 4.6 0.2 - - - +
187L LYS 4.2 0.6 - - - +
190L TYR* 3.8 29.4 - - + -
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Residues in contact with SER 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H LEU* 5.7 1.7 - - - +
150H LEU* 3.4 30.8 - - - +
152H LYS* 3.7 12.8 - - - +
123L PRO 3.9 1.4 - - - +
124L PRO* 3.1 24.5 - - - +
128L GLN* 2.9 29.3 + - - +
133L THR* 4.6 0.7 - - - +
134L ALA* 1.3 72.8 + - - +
136L VAL* 1.3 62.0 + - - +
137L VAL* 4.1 3.8 + - - +
182L THR* 4.3 13.2 - - - +
183L LEU 3.3 6.3 - - - -
184L THR* 4.8 3.3 + - - +
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Residues in contact with VAL 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121L ILE* 4.1 2.5 - - + -
122L PHE 3.5 16.6 - - - +
124L PRO* 3.8 16.8 - - + -
134L ALA 5.0 1.6 - - - -
135L SER* 1.3 77.2 - - - +
137L VAL* 1.3 61.8 + - - +
152L TRP* 3.6 29.4 - - + -
182L THR* 3.5 2.1 - - - +
183L LEU* 2.7 49.3 + - + +
185L LEU* 5.5 2.5 - - + -
190L TYR* 4.2 17.5 - - + -
196L TYR* 4.4 13.7 - - + -
213L PHE* 3.8 19.7 - - + -
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Residues in contact with VAL 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H LEU* 3.9 31.6 - - + -
150H LEU* 4.9 6.3 - - + -
188H SER* 4.2 20.6 - - - +
190H VAL* 5.9 2.0 - - + -
121L ILE* 3.5 4.5 - - - +
122L PHE* 2.8 46.5 + - + -
135L SER* 4.1 4.9 - - - -
136L VAL* 1.3 79.4 - - - +
138L CYS* 1.3 72.2 + - - +
139L LEU* 4.7 2.5 - - + +
152L TRP* 3.8 2.2 - - - -
180L SER* 4.8 8.5 - - - -
181L SER 3.4 6.3 - - - +
182L THR* 3.8 23.6 - - + +
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Residues in contact with CYS 138 (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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119L VAL* 4.0 13.7 - - - -
120L PHE 3.3 10.8 - - - -
121L ILE* 4.6 0.4 - - + +
137L VAL* 1.3 76.1 - - - +
139L LEU* 1.3 61.3 + - - +
140L LEU* 4.1 10.1 + - - +
152L TRP* 3.5 16.8 - - + -
179L LEU 3.7 0.9 - - - +
180L SER* 3.4 5.2 - - - -
181L SER* 2.7 43.2 + - - +
198L CYS* 2.0 52.5 - - + -
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Residues in contact with LEU 139 (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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146H ALA* 3.8 28.0 - - + -
175H PHE* 3.6 32.1 - - + -
190H VAL* 3.7 31.9 - - + -
192H THR* 5.0 1.6 - - + -
118L SER 3.6 0.3 - - - +
119L VAL* 3.2 8.0 - - - +
120L PHE* 2.8 51.6 + - + +
122L PHE* 4.2 13.4 - - + -
137L VAL* 4.2 2.0 - - + -
138L CYS* 1.3 71.6 - - - +
140L LEU* 1.3 64.5 + - - +
141L ASN* 3.8 26.2 - - + +
179L LEU 3.6 2.5 - - - +
180L SER* 4.8 1.3 - - - +
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Residues in contact with LEU 140 (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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117L PRO* 4.1 13.7 - - + -
118L SER 3.7 3.1 - - - -
119L VAL* 4.6 1.1 - - + -
138L CYS* 4.1 15.7 - - - +
139L LEU* 1.3 74.9 - - - +
141L ASN* 1.3 58.9 + - - +
143L PHE* 3.6 15.8 - - + -
148L ALA* 3.9 22.0 - - + -
149L LYS 4.6 1.3 - - - +
150L VAL* 4.4 13.2 - - + -
178L SER* 3.2 6.4 - - - -
179L LEU* 2.8 71.5 + - + +
181L SER* 5.2 0.9 - - - -
200L VAL* 3.5 36.1 - - + -
201L THR 5.8 0.7 - - - +
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Residues in contact with ASN 141 (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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171H SER 5.4 0.5 - - - +
173H HIS* 2.9 21.5 - - - -
190H VAL* 4.8 0.6 - - - +
192H THR* 3.4 27.6 + - - +
117L PRO* 3.5 1.3 - - - +
118L SER* 2.7 54.0 + - - +
120L PHE* 4.4 4.7 - - + -
139L LEU* 3.8 20.6 - - + +
140L LEU* 1.3 72.4 - - - +
142L ASN* 1.3 85.2 + - - +
143L PHE* 3.4 2.6 + - - -
178L SER* 2.7 28.7 + - - -
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Residues in contact with ASN 142 (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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173H HIS* 2.8 30.0 + - - -
192H THR* 5.6 2.0 + - - -
115L ALA* 4.0 7.4 - - - +
116L ALA 3.9 7.8 - - - +
118L SER* 5.5 0.7 - - - +
141L ASN* 1.3 86.2 + - - +
143L PHE* 1.3 60.1 + - - +
174L ASP* 3.8 14.1 + - - +
176L THR* 3.5 28.7 + - + +
177L TYR 3.1 7.7 + - - -
178L SER* 3.0 8.9 + - - -
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Residues in contact with PHE 143 (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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115L ALA* 3.1 13.2 - - - +
117L PRO* 3.6 25.1 - - + -
140L LEU* 3.6 39.3 - - + -
142L ASN* 1.3 76.6 - - - +
144L TYR* 1.3 63.6 + - - +
145L PRO 3.3 19.3 - - - -
146L ARG* 3.2 26.7 - - + -
148L ALA* 4.2 12.6 - - + -
167L VAL* 5.0 4.5 - - + -
176L THR* 3.4 3.1 - - - -
177L TYR* 2.8 59.9 + - + -
178L SER 4.2 1.1 - - - -
179L LEU* 3.7 23.3 - - + -
202L HIS* 3.7 9.9 - + - +
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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