Contacts of the strand formed by residues 169 - 177 (chain C) in PDB entry 6NMY
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 LEU 169 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C PRO* 3.7 37.7 - - + -
134C PRO* 4.4 8.7 - - + -
154C VAL* 5.7 3.4 - - + -
156C LEU* 6.4 1.1 - - + -
164C LEU* 3.7 34.5 - - + -
165C SER 5.9 0.4 - - - +
167C GLY* 3.3 10.5 + - - +
168C ASP* 1.3 90.0 - - + +
170C GLU* 1.3 63.4 + - - +
171C PHE* 4.8 13.8 - - + -
191C ASN* 5.5 4.7 - - - +
214C THR* 4.9 9.0 - - + -
215C ARG 3.4 7.9 - - - +
216C LEU* 3.9 11.7 - - + -
217C ALA* 4.0 3.2 - - - +
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Residues in contact with GLU 170 (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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169C LEU* 1.3 74.9 - - - +
171C PHE* 1.3 67.8 + - - +
189C LEU* 3.4 34.7 - - + +
190C SER 3.6 13.6 + - - +
191C ASN* 4.8 10.8 - - - +
214C THR* 3.6 4.9 - - - -
215C ARG* 2.9 58.7 + - + +
216C LEU 4.4 0.9 - - - +
217C ALA* 4.0 12.4 - - + +
218C PRO* 3.6 27.8 - - - +
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Residues in contact with PHE 171 (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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136C PRO* 4.5 3.8 - - + -
152C TRP* 3.1 48.9 - + + -
154C VAL* 5.0 13.7 - - + -
169C LEU* 4.8 12.3 - - + -
170C GLU* 1.3 84.3 - - - +
172C GLU* 1.3 62.3 + - - +
173C VAL* 4.0 0.9 - - + -
188C LEU 3.6 0.9 - - - +
189C LEU* 3.3 9.2 - - - +
190C SER* 2.9 41.8 + - - +
191C ASN 4.9 1.6 - - - -
192C THR* 3.1 28.5 - - - -
193C SER* 4.5 7.0 - - - -
212C VAL* 5.2 1.8 - - + -
213C ARG 3.4 7.2 - - - +
214C THR* 3.3 33.4 - - + -
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Residues in contact with GLU 172 (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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170C GLU 4.3 0.2 + - - -
171C PHE* 1.3 71.9 - - - +
173C VAL* 1.3 61.7 + - - +
174C VAL* 4.1 17.8 - - + +
187C ILE* 4.2 31.1 - - + +
188C LEU 3.7 2.7 - - - -
189C LEU* 4.8 4.7 - - + +
212C VAL* 3.2 3.2 - - - -
213C ARG* 2.9 77.5 + - + +
215C ARG* 3.1 33.9 + - - +
229C TRP* 3.7 7.6 - - + -
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Residues in contact with VAL 173 (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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150C LEU* 3.9 21.1 - - + -
152C TRP* 4.0 21.1 - - + -
171C PHE 4.9 1.8 - - - +
172C GLU* 1.3 75.9 - - - +
174C VAL* 1.3 68.3 + - - +
175C TYR* 4.1 9.6 - - + -
186C ALA 3.5 0.7 - - - +
187C ILE* 3.4 5.7 - - - +
188C LEU* 2.9 49.0 + - + +
190C SER* 5.0 2.0 - - - -
195C ALA* 4.3 12.8 - - + -
197C LEU* 5.7 0.2 - - + -
210C ALA* 4.6 8.1 - - + -
211C ARG 3.6 4.0 - - - +
212C VAL* 3.6 27.4 - - + -
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Residues in contact with VAL 174 (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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172C GLU* 4.1 13.7 - - + +
173C VAL* 1.3 78.2 - - - +
175C TYR* 1.3 59.3 + - - +
182C TRP* 3.4 25.5 - - + +
185C ALA* 3.4 30.3 - - + -
186C ALA 3.2 4.0 - - - +
187C ILE* 4.2 12.8 - - + -
210C ALA* 3.3 2.0 - - - -
211C ARG* 2.9 40.9 + - + +
229C TRP* 3.4 30.1 - - + -
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Residues in contact with TYR 175 (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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173C VAL* 4.5 9.2 - - + -
174C VAL* 1.3 75.6 - - - +
176C LYS* 1.3 63.9 + - - +
185C ALA* 3.6 0.4 - - - +
186C ALA* 2.9 66.8 + - + +
187C ILE 4.4 3.7 + - - -
188C LEU* 4.1 20.8 - - + +
197C LEU* 3.5 51.1 - - + +
201C HIS* 3.6 34.0 + - - +
202C LEU* 3.9 14.1 - - + -
208C TYR* 4.4 5.8 - + + -
209C VAL 3.2 10.3 - - - +
210C ALA* 4.2 9.6 - - + -
235C TRP* 4.4 4.9 - - + -
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Residues in contact with LYS 176 (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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175C TYR* 1.3 77.1 - - - +
177C ARG* 1.3 93.0 + - - +
178C LEU* 3.8 9.3 + - - +
180C ASP* 3.2 34.8 + - + +
181C SER 3.3 23.6 - - - +
182C TRP* 3.5 40.4 - - + +
185C ALA* 3.7 15.3 - - + +
208C TYR* 3.5 10.2 - - - -
209C VAL* 2.8 48.2 + - - +
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Residues in contact with ARG 177 (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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176C LYS* 1.3 101.9 + - - +
178C LEU* 1.3 59.6 + - - +
179C GLN* 3.0 38.0 + - - +
180C ASP* 2.8 46.8 + - - +
203C MET* 3.4 36.8 - - + +
206C SER* 4.4 13.4 + - - -
207C THR 3.5 7.4 - - - +
208C TYR* 3.5 29.2 - - + +
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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