Contacts of the strand formed by residues 182 - 190 (chain L) in PDB entry 3KYM
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 182 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116L THR* 4.4 14.9 - - - +
149L LYS 3.7 0.2 - - - -
150L ASP* 2.8 32.2 + - - -
151L TYR* 2.8 49.3 + + + +
152L PHE* 3.6 26.5 - + - -
153L PRO* 4.2 0.7 - - + -
154L GLU* 3.4 54.7 + - + +
174L ALA* 4.3 9.0 - - + -
175L VAL 3.7 4.3 - - - -
176L LEU* 3.5 45.2 - - + +
177L GLN* 3.7 2.2 - - - +
181L LEU* 1.3 74.7 - - - +
183L SER* 1.3 59.6 + - - +
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Residues in contact with SER 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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147L LEU* 4.3 10.7 - - - +
148L VAL 3.2 8.7 + - - -
149L LYS* 3.1 28.0 - - - +
151L TYR* 4.2 1.1 - - - -
173L PRO 4.3 0.3 - - - +
174L ALA* 3.5 1.0 - - - -
175L VAL* 2.9 31.1 + - - +
177L GLN* 3.7 25.6 + - - -
182L TYR* 1.3 79.6 - - - +
184L LEU* 1.3 63.7 + - - +
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Residues in contact with LEU 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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147L LEU* 3.8 4.1 - - - +
148L VAL* 2.8 53.2 + - + -
151L TYR* 3.5 24.9 - - + +
155L PRO 4.7 5.6 - - - +
156L VAL* 5.1 5.8 - - + +
158L VAL* 4.6 6.3 - - + -
171L THR* 4.3 16.6 - - + -
172L PHE 3.8 9.9 - - - +
173L PRO 3.6 16.8 - - - +
174L ALA* 3.6 16.2 - - + +
183L SER* 1.3 75.7 + - - +
185L SER* 1.3 75.4 + - - +
186L SER 4.5 0.2 - - - +
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Residues in contact with SER 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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133K VAL* 4.6 10.5 - - - +
176K SER* 4.7 10.3 + - - -
178K THR* 5.1 2.1 + - - -
130L LEU* 3.8 17.5 - - - +
146L CYS 3.2 7.4 - - - -
147L LEU* 3.6 19.4 - - - +
171L THR* 3.7 1.0 - - - -
172L PHE* 3.1 47.6 + - - +
184L LEU* 1.3 81.8 - - - +
186L SER* 1.3 60.4 + - - +
187L VAL* 4.9 2.5 - - - -
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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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145L GLY* 3.0 2.8 - - - -
146L CYS* 2.7 40.5 + - - +
148L VAL* 5.4 0.2 - - - -
158L VAL* 3.8 25.8 - - - +
160L TRP* 3.3 24.3 + - - -
169L VAL* 4.3 0.5 - - - +
170L HIS 3.3 4.4 + - - -
171L THR* 2.8 29.1 + - - -
184L LEU* 4.5 1.2 - - - +
185L SER* 1.3 74.2 - - - +
187L VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 187 (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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133K VAL* 6.1 1.3 - - + -
135K LEU* 3.4 37.0 - - + -
137K ASN* 4.6 9.0 - - - +
130L LEU* 4.6 12.1 - - + -
144L LEU 3.4 9.2 - - - +
145L GLY* 3.8 10.5 - - - +
160L TRP* 4.3 3.6 - - - -
168L GLY 4.8 0.2 - - - -
169L VAL* 3.3 8.5 - - - +
170L HIS* 2.7 51.4 + - + +
172L PHE* 4.1 19.3 - - + -
185L SER* 4.9 2.2 - - - -
186L SER* 1.3 79.7 - - - +
188L VAL* 1.3 64.5 + - - +
189L THR* 5.5 0.4 - - - +
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Residues in contact with VAL 188 (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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142L ALA 3.9 0.2 - - - +
143L ALA* 3.3 28.4 - - - +
144L LEU* 2.8 31.3 + - + +
160L TRP* 4.2 21.8 - - + -
165L LEU* 3.3 32.8 - - + -
167L SER 4.3 2.0 - - - +
168L GLY 3.7 3.6 - - - -
169L VAL* 4.2 14.1 - - + +
187L VAL* 1.3 75.9 - - - +
189L THR* 1.3 67.8 + - - +
190L VAL* 4.1 14.6 - - + -
200L TYR* 4.2 18.2 - - + -
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Residues in contact with THR 189 (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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116K PHE* 5.2 5.4 - - + -
137K ASN* 3.6 37.8 + - + +
138K ASN* 5.6 1.5 + - - +
141L THR* 3.4 25.1 - - + +
142L ALA 3.8 7.2 - - - +
143L ALA* 5.2 4.5 - - + -
167L SER* 4.2 8.8 - - - +
168L GLY* 2.6 34.3 + - - +
170L HIS* 4.8 1.6 - - - -
187L VAL* 5.5 0.9 - - - +
188L VAL* 1.3 76.0 - - - +
190L VAL* 1.3 67.8 + - - +
191L PRO* 4.8 0.9 - - - +
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Residues in contact with VAL 190 (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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141L THR* 2.7 20.7 + - - -
142L ALA 3.0 21.6 + - - +
144L LEU* 5.9 1.1 - - + -
165L LEU* 4.6 7.4 - - + -
167L SER 5.6 0.7 - - - +
188L VAL* 4.1 11.0 - - + +
189L THR* 1.3 81.4 - - - +
191L PRO* 1.4 73.2 - - + +
194L ASN* 4.2 7.9 - - + +
195L PHE* 3.7 28.0 - - + -
200L TYR* 3.4 42.2 - - + +
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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