Contacts of the strand formed by residues 182 - 191 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B PRO* 5.9 2.9 - - - +
116B THR* 5.9 3.0 - - + +
150B ASP* 3.0 23.0 + - - -
151B TYR* 2.9 45.0 + + + +
152B PHE* 3.6 34.2 - + - -
153B PRO* 4.8 0.7 - - + -
154B GLU* 4.0 34.5 - - + +
174B ALA* 3.6 22.9 - - + -
175B VAL 3.8 1.3 - - - -
176B LEU* 3.7 40.1 - - + +
177B GLN* 3.4 0.9 - - - -
181B LEU* 1.3 73.2 - - - +
183B SER* 1.3 59.8 + - - +
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Residues in contact with SER 183 (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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178A THR* 5.6 3.5 - - - +
147B LEU* 4.1 16.8 - - - +
148B VAL 3.1 11.7 + - - -
149B LYS* 4.1 9.8 - - - +
151B TYR* 4.3 0.4 - - - -
174B ALA* 3.8 1.2 - - - -
175B VAL* 3.0 36.8 + - - +
177B GLN* 3.5 24.9 + - - -
182B TYR* 1.3 77.2 - - - +
184B LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 184 (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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147B LEU* 4.9 0.7 - - - -
148B VAL* 2.8 44.2 + - + +
151B TYR* 3.4 27.4 - - + +
154B GLU* 4.5 5.2 - - - +
156B VAL* 4.8 12.6 - - + +
158B VAL* 4.1 16.4 - - + -
171B THR* 3.8 26.5 - - + -
172B PHE* 3.5 23.6 - - - +
173B PRO 4.1 3.1 - - - +
174B ALA* 3.8 16.6 - - + +
175B VAL* 5.9 0.2 - - - -
183B SER* 1.3 77.9 + - - +
185B SER* 1.3 63.9 + - - +
186B SER 4.9 0.2 - - - +
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Residues in contact with SER 185 (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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133A VAL* 4.3 10.2 - - - +
176A SER* 5.2 5.6 - - - -
178A THR* 5.4 0.3 + - - -
130B LEU* 3.4 17.3 - - - +
146B CYS 2.9 14.2 + - - -
147B LEU* 3.3 23.7 - - - +
172B PHE* 3.1 43.0 + - - +
184B LEU* 1.3 79.6 - - - +
186B SER* 1.3 62.9 + - - +
187B VAL* 5.0 1.8 - - - -
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Residues in contact with SER 186 (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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146B CYS* 2.7 40.4 + - - -
148B VAL* 5.5 1.1 - - - -
158B VAL* 3.9 19.7 - - - +
160B TRP* 3.0 30.8 + - - -
169B VAL* 4.9 0.2 - - - +
170B HIS 3.5 7.2 + - - -
171B THR* 3.6 27.5 + - - -
184B LEU* 4.9 0.9 - - - -
185B SER* 1.3 75.9 - - - +
187B VAL* 1.3 59.4 + - - +
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Residues in contact with VAL 187 (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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118A PHE* 4.7 6.5 - - + -
133A VAL* 5.6 2.7 - - + -
135A LEU* 4.0 38.1 - - + -
137A ASN* 4.9 1.6 - - - +
130B LEU* 4.3 19.3 - - + -
143B ALA* 5.7 0.2 - - + -
144B LEU 3.5 10.3 - - - +
160B TRP* 4.5 1.5 + - - -
169B VAL* 3.7 4.7 - - - +
170B HIS* 3.0 49.2 + - + +
172B PHE* 3.7 22.2 - - + -
185B SER* 5.0 2.2 - - - -
186B SER* 1.3 79.7 + - - +
188B VAL* 1.3 66.0 + - - +
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Residues in contact with VAL 188 (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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142B ALA 3.7 1.0 - - - +
143B ALA* 3.4 4.5 - - - -
144B LEU* 2.8 66.8 + - + +
160B TRP* 3.8 22.4 - - + -
165B LEU* 3.7 26.7 - - + -
167B SER 4.3 3.8 - - - +
168B GLY 3.6 4.3 - - - +
169B VAL* 3.8 17.5 - - + -
187B VAL* 1.3 77.4 - - - +
189B THR* 1.3 67.1 + - - +
190B VAL* 3.9 15.2 + - + -
200B TYR* 4.7 1.1 - - + -
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Residues in contact with THR 189 (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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116A PHE* 4.7 5.6 - - + -
135A LEU* 4.7 3.1 - - + -
137A ASN* 3.2 41.5 + - + +
138A ASN* 4.2 6.9 + - - -
141B THR* 4.2 11.4 - - + +
142B ALA 3.3 4.7 - - - +
143B ALA* 4.1 17.9 - - + -
168B GLY* 2.8 35.4 + - - -
170B HIS* 4.6 0.2 + - - -
187B VAL* 4.4 1.1 - - + +
188B VAL* 1.3 74.1 - - - +
190B VAL* 1.3 71.6 + - - +
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Residues in contact with VAL 190 (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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141B THR* 3.9 3.3 + - - -
142B ALA 2.8 22.9 + - - -
144B LEU* 5.1 0.9 - - + -
165B LEU* 5.0 10.3 - - + -
167B SER* 4.3 16.2 - - - +
168B GLY* 5.4 0.2 - - - -
188B VAL* 3.9 19.5 - - + +
189B THR* 1.3 82.1 - - - +
191B PRO* 1.4 69.0 - - + +
194B ASN* 5.8 2.5 - - - +
195B PHE* 2.7 49.4 - - + -
198B GLN* 6.0 0.7 - - - +
200B TYR* 4.0 15.5 - - + +
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Residues in contact with PRO 191 (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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140B SER* 4.5 6.3 - - - +
141B THR* 4.0 15.9 - - - +
190B VAL* 1.4 87.4 - - + +
192B SER* 1.3 56.1 + - - +
193B SER* 3.0 11.3 + - - +
194B ASN* 3.6 17.9 + - - +
195B PHE* 2.9 17.8 - - - -
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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