Contacts of the strand formed by residues 135 - 142 (chain M) 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 GLN 135 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133M ASP 3.5 4.0 + - - +
134M VAL* 1.3 77.6 - - - +
136M TYR* 1.3 68.3 + - - +
160M GLY 3.5 21.2 + - - -
161M THR* 4.1 14.4 - - + -
162M ARG* 3.5 37.0 + - - +
185M ARG 4.0 0.2 - - - +
186M GLY* 3.5 1.4 - - - -
187M ARG* 2.9 62.4 + - - +
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Residues in contact with TYR 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105M ALA 2.7 26.7 + - - -
106M GLY* 3.7 1.1 - - - -
107M ALA* 3.5 22.0 - - + -
124M TRP* 3.6 27.6 - - + +
126M VAL* 3.9 31.0 - - + +
127M GLY 3.2 15.4 + - - -
130M ALA* 4.3 0.2 - - - +
134M VAL* 4.2 21.8 - - + +
135M GLN* 1.3 79.3 - - - +
137M ASP* 1.3 62.6 + - - +
138M LEU 4.2 0.2 - - - -
154M TYR* 4.0 3.9 - - - -
161M THR* 5.5 2.0 - - - -
162M ARG* 3.1 43.4 + - - +
184M VAL* 3.6 21.1 - - + -
185M ARG 3.2 16.8 - - - +
186M GLY* 3.8 10.1 - - - -
193M ILE* 4.3 2.7 - - + -
194M PRO 5.1 0.4 - - - -
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Residues in contact with ASP 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135M GLN 4.2 0.4 + - - -
136M TYR* 1.3 73.6 - - - +
138M LEU* 1.3 60.1 + - - +
139M TYR* 3.6 34.6 + - + +
150M GLU* 4.0 9.0 - - - +
154M TYR* 3.6 8.8 + - - +
162M ARG* 2.9 28.2 + - - -
184M VAL* 3.3 4.6 - - - -
185M ARG* 2.9 36.1 + - + +
187M ARG* 2.8 39.6 + - + -
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Residues in contact with LEU 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M LEU* 5.1 0.2 - - + -
122M CYS* 3.9 19.5 - - + -
124M TRP* 3.5 31.2 - - + -
137M ASP* 1.3 73.0 - - - +
139M TYR* 1.3 77.3 + - - +
140M LEU* 4.3 1.3 - - + +
150M GLU* 3.7 0.5 - - - +
151M CYS* 3.3 32.7 + - + -
154M TYR* 3.2 16.3 + - + -
165M CYS* 4.0 7.2 - - + -
167M PHE* 3.6 35.2 - - + -
182M ILE* 4.2 15.5 - - + -
183M LEU 3.3 11.2 - - - +
184M VAL* 3.8 12.3 - - + -
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Residues in contact with TYR 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137M ASP* 3.6 38.8 + - + +
138M LEU* 1.3 80.3 - - - +
140M LEU* 1.3 60.0 + - - +
141M ASN* 4.0 4.5 + - - +
148M GLN* 3.3 33.4 - - - +
149M TYR 3.4 4.3 - - - -
150M GLU* 3.6 37.9 + - + -
181M HIS 3.9 1.2 - - - +
182M ILE* 3.7 1.2 - - - -
183M LEU* 2.8 43.8 + - + +
185M ARG* 3.2 45.0 + - + -
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Residues in contact with LEU 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120M LEU* 3.6 31.2 - - + -
138M LEU* 4.3 0.6 - - + +
139M TYR* 1.3 73.9 - - - +
141M ASN* 1.3 63.6 + - - +
142M VAL* 3.8 10.5 - - + -
148M GLN* 3.5 4.5 - - - +
149M TYR* 2.9 35.4 + - + +
167M PHE* 3.8 35.0 - - + -
170M ILE* 4.2 8.5 - - + -
173M LEU* 3.6 24.0 - - + -
180M SER* 3.3 25.4 - - - +
181M HIS 3.7 3.1 - - - -
182M ILE* 4.2 11.9 - - + +
202M PHE* 5.4 1.6 - - + -
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Residues in contact with ASN 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139M TYR* 4.0 10.9 + - - +
140M LEU* 1.3 77.1 - - - +
142M VAL* 1.3 62.3 + - - +
147M GLN 4.3 6.2 - - - +
148M GLN* 3.1 32.3 + - - +
180M SER* 2.6 27.3 + - - -
181M HIS* 2.9 50.8 + - + +
183M LEU* 4.9 6.5 - - - +
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Residues in contact with VAL 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140M LEU* 3.8 18.4 - - + -
141M ASN* 1.3 81.5 - - - +
143M ALA* 1.3 69.1 + - - +
145M ARG* 3.2 50.9 - - + +
147M GLN 3.8 13.1 + - - +
149M TYR* 4.5 5.8 - - + -
173M LEU* 4.0 18.8 - - + +
174M SER* 4.2 16.4 - - - -
177M SER* 4.3 9.6 - - - +
179M SER 4.2 6.3 - - - +
180M SER* 4.6 4.0 - - - +
181M HIS* 6.4 0.2 - - - -
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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