Contacts of the strand formed by residues 177 - 186 (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 TYR 177 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173H HIS* 5.9 0.9 - - - -
107L LYS* 6.0 1.4 - - - +
109L GLU* 2.3 43.4 + - - +
142L ASN* 3.1 6.0 + - - -
143L PHE* 2.8 57.1 + - + -
144L TYR* 3.9 14.4 - + - -
146L ARG* 3.6 53.2 - - + -
167L VAL* 4.2 8.1 - - + -
168L THR* 3.6 22.4 - - - -
169L GLU* 5.0 0.9 - - - -
170L GLN* 3.7 36.2 + - + +
176L THR* 1.3 74.4 - - - +
178L SER* 1.3 63.0 + - - +
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Residues in contact with SER 178 (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* 3.2 14.0 + - - -
175H PHE* 3.5 14.7 - - - -
140L LEU 3.2 7.6 - - - -
141L ASN* 2.7 33.2 + - - -
142L ASN* 3.0 18.7 + - - -
143L PHE* 3.7 2.9 - - - -
167L VAL* 3.3 6.9 - - - +
168L THR* 3.0 36.4 + - - -
177L TYR* 1.3 70.8 - - - +
179L LEU* 1.3 60.6 + - - +
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Residues in contact with LEU 179 (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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175H PHE* 3.5 5.6 - - - -
138L CYS 3.7 0.5 - - - +
139L LEU* 3.6 5.5 - - - +
140L LEU* 2.8 61.6 + - + +
143L PHE* 3.9 15.9 - - + -
148L ALA* 4.9 9.2 - - + +
150L VAL* 3.9 22.2 - - + -
165L GLU* 4.2 18.4 - - + -
166L SER 3.3 13.9 - - - +
167L VAL* 2.6 37.5 - - + -
178L SER* 1.3 74.1 - - - +
180L SER* 1.3 66.0 + - - +
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Residues in contact with SER 180 (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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175H PHE* 3.4 25.5 - - - +
188H SER* 5.2 6.9 + - - -
137L VAL* 4.8 12.3 - - - -
138L CYS 3.4 6.1 - - - -
139L LEU* 4.8 1.1 - - - +
140L LEU* 5.5 0.2 - - - -
164L GLN 5.1 0.9 + - - -
165L GLU* 3.1 9.0 - - - +
166L SER* 2.8 47.9 + - - -
179L LEU* 1.3 76.5 - - - +
181L SER* 1.3 61.9 + - - +
182L THR* 4.2 6.6 + - - -
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Residues in contact with SER 181 (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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137L VAL* 3.4 2.9 - - - +
138L CYS* 2.7 51.3 + - - -
140L LEU* 5.2 1.6 - - - -
150L VAL* 3.9 23.6 - - - +
152L TRP* 2.9 29.3 + - - -
164L GLN 3.5 3.1 - - - -
165L GLU* 2.8 22.9 + - - -
180L SER* 1.3 74.4 - - - +
182L THR* 1.3 60.8 + - - +
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Residues in contact with THR 182 (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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150H LEU* 5.2 8.5 - - + +
152H LYS* 6.3 1.3 - - + -
186H SER* 5.9 1.3 - - - +
188H SER* 4.8 5.0 + - - -
135L SER* 4.3 12.8 - - - +
136L VAL 3.5 7.6 - - - +
137L VAL* 3.8 22.0 - - + +
152L TRP* 4.4 0.4 - - - -
162L ASN 3.7 0.7 - - - +
163L SER* 3.1 25.2 - - - -
164L GLN* 2.8 21.6 + - - -
180L SER* 4.6 7.6 + - - -
181L SER* 1.3 74.2 + - - +
183L LEU* 1.3 68.9 + - - +
184L THR* 3.9 11.0 + - - +
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Residues in contact with LEU 183 (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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134L ALA 3.5 1.6 - - - +
135L SER* 3.3 5.9 - - - -
136L VAL* 2.7 52.8 + - + +
152L TRP* 3.7 51.8 - - + +
154L VAL* 4.1 24.5 - - + -
159L GLN* 4.5 0.2 - - + -
162L ASN* 3.2 47.1 - - + +
181L SER 4.1 0.6 + - - -
182L THR* 1.3 71.5 - - - +
184L THR* 1.3 60.2 + - - +
185L LEU* 4.0 13.4 + - + -
196L TYR* 4.6 3.1 - - + -
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Residues in contact with THR 184 (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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152H LYS* 4.6 16.2 + - - +
180H GLN* 5.3 1.7 + - - -
133L THR* 4.1 22.7 - - + +
134L ALA 3.5 2.5 - - - +
135L SER* 4.8 2.5 + - - +
162L ASN* 3.0 25.8 + - - +
182L THR* 4.3 13.0 + - - +
183L LEU* 1.3 74.4 + - - +
185L LEU* 1.3 72.1 - - - +
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Residues in contact with LEU 185 (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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133L THR* 3.4 6.0 - - - +
134L ALA* 2.5 44.7 + - + +
136L VAL* 5.5 1.8 - - + -
154L VAL* 4.8 5.4 - - + -
159L GLN* 4.6 5.2 - - - +
162L ASN* 3.8 22.0 - - + +
183L LEU* 4.5 13.7 - - + +
184L THR* 1.3 85.1 - - - +
186L SER* 1.3 65.2 + - - +
189L ASP* 4.5 11.2 - - + +
190L TYR* 3.9 19.3 - - + +
193L HIS* 5.5 1.6 - - + -
196L TYR* 3.7 36.1 - - + +
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Residues in contact with SER 186 (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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132L GLY 3.6 12.6 - - - -
133L THR* 4.3 1.8 - - - +
185L LEU* 1.3 75.6 - - - +
187L LYS* 1.3 66.1 + - - +
188L ALA* 3.7 8.7 + - - +
189L ASP* 2.9 44.2 + - - +
190L TYR* 2.8 21.5 + - - +
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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