Contacts of the strand formed by residues 209 - 218 (chain C) in PDB entry 5TIN
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 CYS 209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C GLN* 4.0 11.7 - - - -
156C LEU 3.2 10.5 - - - -
157C GLU* 3.8 23.6 - - + -
168C PHE* 5.2 0.2 - - - -
197C TYR* 3.6 6.4 - - - +
198C CYS* 2.1 79.9 + - - +
199C THR* 3.8 5.6 + - - +
200C LYS* 3.9 7.9 - - + -
207C PHE 3.6 4.6 + - - +
208C THR* 1.3 79.6 + - - +
210C ILE* 1.3 66.8 + - - +
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Residues in contact with ILE 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C CYS* 4.2 11.7 - - + -
154C MET 3.9 0.2 - - - +
155C GLN* 3.5 2.1 - - - -
156C LEU* 2.7 50.7 + - + +
168C PHE* 3.6 32.5 - - + +
169C GLU* 3.9 12.3 - - - +
170C TRP* 3.6 52.9 - - + +
196C ARG 3.5 5.4 - - - +
197C TYR* 4.0 20.0 - - + -
198C CYS* 3.5 1.6 - - - -
208C THR* 5.1 0.4 - - - +
209C CYS* 1.3 79.9 - - - +
211C GLU* 1.3 61.7 + - - +
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Residues in contact with GLU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ILE* 4.0 13.2 - - + +
154C MET 3.3 10.3 - - - +
155C GLN* 3.0 30.4 + - + -
170C TRP* 3.1 13.2 + - - -
194C ASP 4.5 0.2 - - - -
195C LEU* 3.5 1.2 - - - -
196C ARG* 2.9 47.1 + - + +
197C TYR 5.0 0.8 - - - +
198C CYS* 3.5 16.2 - - + +
210C ILE* 1.3 77.2 - - - +
212C VAL* 1.3 70.4 + - - +
213C ARG* 2.8 41.4 + - + +
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Residues in contact with VAL 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ILE* 4.6 3.4 - - + -
152C CYS 4.0 0.5 - - - +
153C ILE* 3.3 4.7 - - - +
154C MET* 3.0 55.2 + - + +
170C TRP* 3.7 24.2 - - + -
176C VAL* 4.0 10.3 - - + -
193C LYS* 4.0 21.5 - - + -
194C ASP 3.4 8.1 - - - +
195C LEU* 4.0 9.9 - - + -
211C GLU* 1.3 74.8 - - - +
213C ARG* 1.3 65.1 + - - +
214C PHE* 3.9 24.3 - - + -
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Residues in contact with ARG 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C THR* 3.8 30.9 - - + +
152C CYS 3.6 3.8 - - - -
153C ILE* 3.9 17.3 - - + +
193C LYS* 3.4 11.4 - - - +
194C ASP* 2.8 54.5 + - - +
196C ARG* 3.3 41.7 - - + +
211C GLU* 2.8 32.6 + - + +
212C VAL* 1.3 75.8 - - - +
214C PHE* 1.3 63.1 + - - +
215C HIS* 4.2 2.9 + - - +
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Residues in contact with PHE 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ILE* 4.5 2.5 - - + -
45C ILE* 3.5 33.7 - - + -
48C PHE* 4.0 24.0 - + + -
58C TYR* 4.0 18.2 - - - -
150C GLN 3.7 0.3 - - - +
151C THR* 3.3 6.9 - - - +
152C CYS* 2.8 45.9 + - + +
154C MET* 4.1 15.9 - - + -
176C VAL* 4.2 3.6 - - + -
189C LEU* 3.9 19.7 - - + -
193C LYS* 3.7 33.2 - - + -
212C VAL* 3.9 31.4 - - + -
213C ARG* 1.3 74.4 - - - +
215C HIS* 1.3 63.0 + - - +
216C LEU* 4.0 2.9 + - + +
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Residues in contact with HIS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C VAL* 4.8 10.3 - - + +
150C GLN 3.5 3.1 + - - +
151C THR* 3.3 31.5 + - + -
188C LEU 3.5 0.2 - - - +
189C LEU* 3.7 5.7 - - - +
190C LYS* 3.0 48.9 + - + +
192C GLU* 3.6 29.4 + - + -
194C ASP* 2.7 34.6 + - - -
213C ARG* 4.3 4.3 + - - -
214C PHE* 1.3 74.4 + - - +
216C LEU* 1.3 61.1 + - - +
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Residues in contact with LEU 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C PHE* 4.2 13.2 - - + -
51C ILE* 3.9 21.8 - - + -
149C VAL* 3.3 6.5 - - - +
150C GLN* 2.9 43.3 + - + +
152C CYS* 3.7 32.3 - - + -
184C LEU* 3.8 27.6 - - + -
187C PHE* 3.7 22.4 - - + -
188C LEU 3.4 1.1 - - - -
189C LEU* 4.0 27.1 - - + -
214C PHE 4.8 2.7 - - - +
215C HIS* 1.3 73.9 - - - +
217C GLU* 1.3 61.6 + - - +
218C ARG 3.9 0.5 + - - -
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Residues in contact with GLU 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ASP 4.3 5.2 - - - +
149C VAL* 4.3 11.9 - - + -
187C PHE* 3.3 2.7 - - - -
188C LEU* 2.8 58.5 + - + +
190C LYS* 3.7 30.3 + - + +
215C HIS 4.1 0.8 + - - -
216C LEU* 1.3 71.7 - - - +
218C ARG* 1.3 70.4 + - - +
219C GLN 3.5 0.3 + - - -
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Residues in contact with ARG 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C GLU* 3.0 39.0 + - - +
140C MET* 4.8 0.8 - - - -
142C LEU* 4.2 3.4 - - - +
145C PHE* 3.6 14.5 - - - -
146C PRO* 3.4 22.5 - - - +
147C MET* 5.5 2.4 - - - -
148C ASP* 2.6 60.6 + - - +
150C GLN* 4.8 3.8 - - - +
186C GLN* 3.6 21.4 + - + +
187C PHE* 3.5 26.9 - - + -
216C LEU 3.9 0.2 + - - -
217C GLU* 1.3 80.2 - - - +
219C GLN* 1.3 70.9 + - - +
220C MET* 3.7 2.6 + - - +
223C TYR* 3.6 32.2 + - + -
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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