Contacts of the helix formed by residues 193 - 210 (chain K) in PDB entry 6T90
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 SER 193 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128J T 3.0 30.2 + - - -
192K LEU* 1.3 79.0 - - - +
194K PHE* 1.3 72.1 + - - +
195K LYS* 3.6 4.8 + - - +
196K ASN* 3.2 23.4 + - - +
197K MET* 3.0 21.9 + - - +
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Residues in contact with PHE 194 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K ILE* 4.4 24.9 - - + -
142K LEU* 4.4 21.5 - - + -
146K LEU* 4.3 3.1 - - + +
192K LEU 3.9 0.2 + - - -
193K SER* 1.3 80.8 - - - +
195K LYS* 1.3 96.6 + - + +
197K MET* 3.4 15.7 + - + +
198K CYS* 3.0 35.3 + - - -
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Residues in contact with LYS 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J T 4.9 7.0 - - - +
193K SER* 3.2 7.9 + - - +
194K PHE* 1.3 107.2 - - + +
196K ASN* 1.3 64.5 + - - +
198K CYS* 3.3 6.0 + - - +
199K LYS* 2.9 50.8 + - - +
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Residues in contact with ASN 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J T 2.8 56.9 + - - +
129J T 4.3 8.9 + - - +
192K LEU* 4.3 22.4 - - + +
193K SER* 3.2 25.3 + - - +
195K LYS* 1.3 80.4 - - - +
197K MET* 1.3 59.0 + - - +
199K LYS* 4.0 10.2 + - - +
200K LEU* 2.9 33.1 + - - +
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Residues in contact with MET 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K LEU* 3.9 31.6 - - + +
187K PHE* 3.8 29.8 - - + +
190K LEU* 3.5 47.3 - - + +
192K LEU* 3.4 31.2 - - + +
193K SER 3.0 16.3 + - - +
194K PHE* 3.8 7.2 - - + +
195K LYS 3.2 0.2 - - - -
196K ASN* 1.3 77.5 - - - +
198K CYS* 1.3 56.7 + - - +
201K ARG* 2.8 33.3 + - - +
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Residues in contact with CYS 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K LEU* 3.8 38.8 - - - -
146K LEU* 4.2 8.3 - - - -
194K PHE* 3.0 26.2 + - - +
195K LYS* 3.7 6.7 - - - +
197K MET* 1.3 78.1 - - - +
199K LYS* 1.3 57.9 + - + +
201K ARG* 3.8 19.1 + - - +
202K PRO* 3.1 24.6 - - - +
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Residues in contact with LYS 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195K LYS* 2.9 35.3 + - - +
196K ASN* 4.0 10.0 + - - +
198K CYS* 1.3 79.7 - - + +
200K LEU* 1.3 59.6 + - - +
202K PRO* 3.4 10.7 - - - +
203K LEU* 3.9 11.6 - - - +
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Residues in contact with LEU 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J T 5.9 2.0 - - - +
171K LEU* 4.3 5.6 - - + -
179K PHE* 3.6 39.3 - - + -
183K THR* 4.2 24.0 - - + -
184K ILE* 5.1 4.7 - - + -
187K PHE* 4.1 15.7 - - + -
192K LEU* 5.0 4.5 - - + -
196K ASN 2.9 18.2 + - - +
197K MET* 4.2 2.7 - - - +
199K LYS* 1.3 76.7 - - - +
201K ARG* 1.3 68.0 + - - +
203K LEU* 2.9 29.8 + - + +
204K LEU* 3.2 29.8 + - + +
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Residues in contact with ARG 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K LEU* 4.4 7.9 - - - +
145K GLU* 3.1 38.6 + - - +
146K LEU* 4.1 23.3 - - + +
149K PHE* 4.1 24.0 - - + -
187K PHE* 5.0 1.8 - - + -
197K MET 2.8 20.7 + - - +
198K CYS* 3.8 18.5 + - - +
200K LEU* 1.3 74.1 - - - +
202K PRO* 1.3 59.7 - - + +
204K LEU* 2.9 15.1 + - - +
205K GLN* 2.7 60.4 + - + +
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Residues in contact with PRO 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175K PHE* 4.5 2.1 - - - -
198K CYS 3.1 19.3 - - - +
199K LYS* 3.4 8.3 - - - +
200K LEU 3.4 3.8 - - - -
201K ARG* 1.3 98.6 - - + +
203K LEU* 1.3 65.8 + - + +
205K GLN* 3.6 19.3 + - - +
206K LYS* 3.2 20.8 + - - +
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Residues in contact with LEU 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K LEU* 3.1 18.9 - - + +
175K PHE* 3.7 50.0 - - + -
177K LYS* 4.4 15.0 - - + +
179K PHE* 3.9 29.4 - - + -
199K LYS 3.9 18.4 - - - +
200K LEU* 2.9 16.2 + - + +
202K PRO* 1.3 83.5 - - + +
204K LEU* 1.3 59.4 + - - +
206K LYS* 3.3 5.0 + - - +
207K TRP 3.0 20.6 + - - -
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Residues in contact with LEU 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K PHE* 3.6 13.7 - - + -
153K LEU* 3.9 14.9 - - + +
167K VAL* 3.7 30.3 - - + -
171K LEU* 3.9 13.7 - - + -
184K ILE* 4.2 8.3 - - + -
187K PHE* 3.5 45.1 - - + -
200K LEU* 3.7 31.0 - - + +
201K ARG 2.9 6.0 + - - +
203K LEU* 1.3 77.3 - - - +
205K GLN* 1.3 63.2 + - - +
207K TRP* 3.1 4.8 + - - +
208K VAL* 3.0 27.5 + - - +
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Residues in contact with GLN 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K GLU* 5.3 3.0 + - - -
149K PHE* 3.5 26.4 - - + -
201K ARG* 2.7 46.6 + - + +
202K PRO* 3.7 17.3 - - - +
204K LEU* 1.3 75.0 - - - +
206K LYS* 1.3 63.3 + - - +
208K VAL* 3.2 6.8 + - - +
209K GLU* 3.1 31.5 + - - +
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Residues in contact with LYS 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174K LEU* 4.0 16.6 - - + -
175K PHE* 3.7 22.7 - - + -
202K PRO 3.2 11.5 + - - +
203K LEU 3.5 8.7 - - - +
204K LEU 3.2 0.4 - - - -
205K GLN* 1.3 79.1 - - - +
207K TRP* 1.3 62.6 + - - +
209K GLU* 3.1 22.5 + - - +
210K GLU* 3.0 53.5 + - - +
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Residues in contact with TRP 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K LEU* 3.6 25.6 - - + -
156K LYS* 4.9 3.6 - - + -
157K ARG* 3.9 32.1 - - + -
160K LEU* 5.0 5.4 - - + -
162K TYR* 3.7 43.5 - + + -
167K VAL* 3.7 38.4 - - + +
170K THR* 3.5 42.3 + - + +
171K LEU* 4.0 10.1 - - + -
174K LEU* 4.6 6.7 - - - +
203K LEU 3.0 14.2 + - - +
204K LEU* 3.1 11.2 + - + +
206K LYS* 1.3 78.0 - - - +
208K VAL* 1.3 73.2 + - + +
210K GLU* 3.5 14.5 + - - +
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Residues in contact with VAL 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K PHE* 4.5 10.1 - - + -
152K LEU* 5.3 3.4 - - + +
153K LEU* 3.5 37.0 - - + +
156K LYS* 4.1 28.2 - - + +
160K LEU* 5.3 9.2 - - - +
204K LEU 3.0 18.0 + - - +
205K GLN* 3.2 7.8 + - - +
207K TRP* 1.3 87.4 - - + +
209K GLU* 1.3 64.2 + - + +
210K GLU 3.6 2.6 + - - -
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Residues in contact with GLU 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205K GLN* 3.1 20.2 + - - +
206K LYS* 3.5 28.3 + - + +
208K VAL* 1.3 79.9 - - + +
210K GLU* 1.3 62.2 + - + +
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Residues in contact with GLU 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170K THR* 5.6 4.5 - - + -
174K LEU* 4.2 23.0 - - + +
206K LYS* 3.0 58.8 + - + +
207K TRP* 3.5 11.6 + - - +
208K VAL 3.4 3.0 - - - -
209K GLU* 1.3 82.7 - - - +
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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