Contacts of the strand formed by residues 169 - 177 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A VAL* 6.0 0.7 - - + -
133A PRO* 3.6 42.4 - - + -
134A PRO* 4.4 10.1 - - + -
154A VAL* 5.3 6.7 - - + -
155A ALA 6.0 1.1 - - - +
164A LEU* 3.5 36.8 - - + -
165A SER 4.9 0.4 - - - +
166A PRO* 3.9 17.8 + - + +
167A GLY* 3.4 4.4 - - - +
168A ASP* 1.3 86.7 - - + +
170A GLU* 1.3 63.0 + - - +
171A PHE* 4.9 12.8 - - + -
191A ASN* 5.0 6.9 - - - +
214A THR* 4.6 10.8 - - + -
215A ARG 3.4 9.9 - - - +
216A LEU* 4.6 2.7 - - - -
217A ALA* 4.0 3.2 - - - +
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 1.3 75.5 - - - +
171A PHE* 1.3 67.4 + - - +
189A LEU* 3.3 20.5 - - + +
190A SER 3.7 13.0 - - - +
191A ASN* 4.6 13.3 - - - +
214A THR* 3.6 4.2 - - - -
215A ARG* 2.5 78.7 + - + +
216A LEU 4.0 0.2 - - - +
217A ALA* 4.0 9.7 - - + +
218A PRO* 3.8 25.7 - - - +
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Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PRO* 4.6 0.9 - - + -
152A TRP* 3.1 48.2 - + + -
154A VAL* 4.3 20.4 - - + -
166A PRO 6.2 0.2 - - - -
169A LEU* 4.9 11.9 - - + -
170A GLU* 1.3 82.4 - - - +
172A GLU* 1.3 60.0 + - - +
173A VAL 4.0 0.2 - - - -
188A LEU 3.7 0.9 - - - +
189A LEU* 3.3 8.7 - - - +
190A SER* 2.9 41.2 + - - +
191A ASN 4.7 3.1 - - - -
192A THR* 3.1 29.4 - - - -
193A SER* 4.4 6.3 - - - -
212A VAL* 4.1 9.2 - - + -
213A ARG 3.5 1.8 - - - -
214A THR* 3.4 35.2 - - + -
215A ARG* 4.9 0.7 - - - -
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PHE* 1.3 72.3 - - - +
173A VAL* 1.3 62.4 + - - +
174A VAL* 4.4 15.3 - - + +
187A ILE* 4.3 29.7 - - + +
188A LEU 3.7 2.9 - - - +
189A LEU* 4.8 7.0 - - + +
212A VAL* 3.2 2.7 - - - -
213A ARG* 2.9 78.2 + - + +
215A ARG* 3.3 28.0 + - - +
229A TRP* 3.8 7.7 - - + -
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 3.8 24.7 - - + -
152A TRP* 3.8 22.4 - - + -
171A PHE 5.1 1.8 - - - +
172A GLU* 1.3 73.0 - - - +
174A VAL* 1.3 69.5 + - - +
175A TYR* 4.2 10.5 - - + -
186A ALA 3.6 0.7 - - - +
187A ILE* 3.5 5.0 - - - +
188A LEU* 2.9 51.1 + - + +
190A SER* 5.1 1.6 - - - -
195A ALA* 4.3 11.4 - - + -
197A LEU* 5.5 0.2 - - + -
210A ALA* 4.7 5.8 - - + -
211A ARG 3.6 8.5 - - - +
212A VAL* 3.6 22.4 - - + +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLU* 4.4 7.9 - - + +
173A VAL* 1.3 79.8 - - - +
175A TYR* 1.3 61.7 + - - +
182A TRP* 3.6 24.4 - - + +
185A ALA* 3.5 27.4 - - + -
186A ALA 3.2 6.1 - - - +
187A ILE* 4.4 15.3 - - + -
210A ALA* 3.3 2.3 - - - -
211A ARG* 2.9 41.9 + - + +
229A TRP* 3.5 31.0 - - + -
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Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A VAL* 4.5 10.3 - - + -
174A VAL* 1.3 75.5 - - - +
176A LYS* 1.3 64.2 + - - +
185A ALA* 3.5 0.3 - - - +
186A ALA* 2.9 67.9 + - + +
187A ILE 4.3 4.5 + - - -
188A LEU* 4.1 17.9 - - + +
197A LEU* 3.6 50.0 - - + +
201A HIS* 3.8 34.8 + - - +
202A LEU* 4.0 12.8 - - + -
208A TYR* 4.5 6.0 - + + -
209A VAL 3.3 10.8 - - - +
210A ALA* 4.2 9.2 - - + -
235A TRP* 4.5 5.4 - - + -
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Residues in contact with LYS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TYR* 1.3 79.0 - - - +
177A ARG* 1.3 89.9 + - - +
178A LEU* 3.4 11.5 + - - +
180A ASP* 3.3 35.1 + - + +
181A SER 3.3 22.2 - - - +
182A TRP* 3.4 45.5 - - + +
185A ALA* 3.7 14.6 - - + +
208A TYR* 3.4 10.5 - - - -
209A VAL* 2.8 47.3 + - - +
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Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LYS* 1.3 100.5 + - - +
178A LEU* 1.3 58.4 + - - +
179A GLN* 3.0 35.1 + - - +
180A ASP* 3.0 42.4 + - - +
203A MET* 4.3 18.3 - - - +
206A SER* 4.3 18.5 + - - -
207A THR 3.5 7.9 - - - +
208A TYR* 3.4 36.2 - - + +
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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