Contacts of the strand formed by residues 182 - 190 (chain B) in PDB entry 1KTD
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 PHE 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ASP 5.4 0.9 - - - -
29A ASP* 4.6 3.1 - - - -
148B ASP* 3.0 23.2 + - - -
149B PHE* 2.8 43.2 + - + -
150B TYR* 3.7 22.4 - + - -
151B PRO 4.0 0.2 - - - -
152B GLY* 3.5 29.8 - - - -
174B LEU* 3.5 34.3 - - + -
175B VAL 3.1 15.0 - - - +
176B ARG* 3.7 53.6 - - + -
177B ASN* 3.8 3.8 + - - +
181B THR* 1.3 78.7 - - - +
183B GLN* 1.3 61.8 + - - +
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Residues in contact with GLN 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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92A LEU* 4.0 6.9 - - - +
93A SER* 3.0 27.2 + - - +
94A ARG 3.0 15.1 + - - +
95A SER* 4.6 5.0 - - - -
96A PRO* 5.4 1.0 - - - +
146B VAL 3.4 8.1 - - - -
147B SER* 3.9 18.4 - - - +
149B PHE* 3.4 3.8 - - - -
174B LEU* 4.2 0.5 - - - -
175B VAL* 2.9 54.0 + - + +
177B ASN* 2.9 22.5 + - - +
182B PHE* 1.3 77.6 - - - +
184B THR* 1.3 62.9 + - - +
185B LEU* 5.9 3.8 - - - +
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Residues in contact with THR 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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144B CYS 4.0 0.2 - - - +
145B SER* 4.6 0.2 + - - -
146B VAL* 2.8 53.4 + - + +
149B PHE* 4.2 11.9 - - + -
154B ILE* 5.1 5.2 - - + -
156B VAL* 4.4 15.5 - - + -
171B SER* 3.8 4.9 + - - -
172B THR* 3.7 3.5 + - - -
173B GLY 2.8 27.0 + - - -
174B LEU* 4.6 3.8 - - - -
175B VAL* 5.3 0.4 - - - -
183B GLN* 1.3 79.2 - - - +
185B LEU* 1.3 74.9 + - - +
186B VAL* 4.2 6.5 - - + +
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Residues in contact with LEU 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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129B TYR* 4.4 11.9 - - - +
143B VAL* 3.9 15.7 - - + -
144B CYS 3.5 2.0 - - - +
145B SER* 3.7 33.7 - - - +
170B VAL 3.9 0.6 - - - +
171B SER* 3.3 7.3 + - - -
172B THR* 3.1 48.7 + - + +
183B GLN* 5.9 3.8 - - - +
184B THR* 1.3 77.2 + - - +
186B VAL* 1.3 61.7 + - - +
187B MET* 4.0 17.0 - - + -
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Residues in contact with VAL 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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144B CYS* 3.0 23.9 + - - +
156B VAL* 3.4 50.0 - - + +
157B ARG* 5.7 0.2 - - - -
158B TRP* 2.9 37.4 + - + -
169B ILE* 4.5 20.6 - - + -
170B VAL 3.7 2.5 - - - -
171B SER* 4.1 13.5 - - - +
184B THR* 4.2 10.1 - - + +
185B LEU* 1.3 78.3 - - - +
187B MET* 1.3 61.6 + - - +
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Residues in contact with MET 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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131B THR* 5.7 1.1 - - - -
141B LEU* 3.3 37.5 - - + -
142B LEU 3.0 4.9 - - - +
143B VAL* 3.7 29.4 - - + -
158B TRP* 3.9 2.2 - - - -
168B GLY 3.4 0.9 - - - +
169B ILE* 3.3 6.4 - - - +
170B VAL* 2.6 72.6 + - + +
172B THR* 4.2 15.5 - - + -
185B LEU* 4.2 15.3 - - + +
186B VAL* 1.3 76.8 - - - +
188B LEU* 1.3 60.7 + - - +
21D VAL* 4.1 16.4 - - + -
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Residues in contact with LEU 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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140B ASN 3.8 1.7 - - - +
141B LEU* 3.1 6.1 - - - +
142B LEU* 2.7 45.6 + - + +
158B TRP* 3.7 34.0 - - + +
165B GLU* 3.5 25.1 - - + -
167B THR 4.3 2.9 - - - +
168B GLY 3.4 2.2 - - - +
169B ILE* 3.4 26.7 - - + -
187B MET* 1.3 74.1 - - - +
189B GLU* 1.3 65.6 + - - +
190B THR* 3.3 30.9 + - + +
198B TYR* 3.6 23.6 - - + -
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Residues in contact with GLU 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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139B HIS* 4.9 27.5 - - + +
140B ASN 4.6 2.9 - - - -
141B LEU* 3.7 23.9 - - + +
167B THR 5.0 0.3 - - - +
168B GLY* 2.7 44.0 + - - +
169B ILE 4.9 0.3 - - - +
170B VAL* 3.4 23.0 - - + +
188B LEU* 1.3 73.8 - - - +
190B THR* 1.3 68.1 + - - +
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Residues in contact with THR 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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139B HIS* 4.7 3.7 + - - +
140B ASN* 2.6 45.8 + - - +
142B LEU* 4.8 4.7 - - - +
160B ARG* 3.4 19.5 - - - +
165B GLU* 3.8 7.4 - - - +
188B LEU* 3.3 33.0 + - + +
189B GLU* 1.3 81.5 - - - +
191B VAL* 1.3 66.8 + - - +
192B PRO* 4.2 4.2 - - - +
198B TYR* 3.3 28.7 + - + -
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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