Contacts of the strand formed by residues 179 - 187 (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 SER 179 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46I ASP* 5.6 1.9 + - - -
49I MET* 4.0 27.7 - - - +
142M VAL* 4.2 1.4 - - - -
143M ALA* 3.3 37.2 + - - +
177M SER* 4.2 4.9 - - - +
178M GLN* 1.3 79.7 - - - +
180M SER* 1.3 65.7 + - - +
200M VAL 3.3 11.2 - - - -
201M VAL* 4.3 3.4 - - - +
202M PHE* 3.8 8.2 - - - -
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Residues in contact with SER 180 (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* 3.3 22.4 - - - +
141M ASN 2.6 23.3 + - - -
142M VAL* 4.6 2.2 - - - +
143M ALA* 4.8 1.6 - - - +
179M SER* 1.3 78.4 - - - +
181M HIS* 1.3 63.5 + - - +
182M ILE* 4.3 1.6 - - - +
199M PHE* 3.6 7.7 - - - +
200M VAL* 2.9 40.4 + - - +
202M PHE* 3.4 26.5 - - - -
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Residues in contact with HIS 181 (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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75M LEU* 3.4 28.5 - - + +
140M LEU* 3.7 0.2 - - - -
141M ASN* 2.9 55.5 + - + +
142M VAL 5.6 0.2 - - - -
180M SER* 1.3 76.3 + - - +
182M ILE* 1.3 71.9 + - - +
183M LEU* 4.2 9.9 - - + +
197M ASP* 3.4 33.0 + - - +
198M LYS 3.7 4.3 - - - -
199M PHE* 3.1 36.3 - + + -
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Residues in contact with ILE 182 (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* 4.6 13.1 - - + +
112M CYS* 3.5 38.6 - - + -
120M LEU* 4.4 15.0 - - + -
122M CYS* 3.8 6.3 - - - -
138M LEU* 4.2 26.2 - - + -
139M TYR 3.7 2.7 - - - -
140M LEU* 4.2 18.2 - - + -
180M SER* 4.3 3.8 - - - +
181M HIS* 1.3 75.0 - - - +
183M LEU* 1.3 64.9 + - - +
197M ASP* 3.1 5.9 - - - +
198M LYS* 2.9 38.3 + - + +
200M VAL* 3.8 24.9 - - + -
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Residues in contact with LEU 183 (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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75M LEU* 5.7 10.1 - - + -
76M CYS* 3.5 32.3 - - - -
138M LEU* 3.3 1.7 - - - +
139M TYR* 2.8 43.5 + - + +
141M ASN* 4.9 7.2 - - - +
181M HIS* 4.2 17.7 - - + +
182M ILE* 1.3 75.7 - - - +
184M VAL* 1.3 83.7 + - - +
185M ARG* 3.5 40.8 - - + +
195M CYS* 3.5 13.9 - - + -
196M THR 3.6 3.4 - - - +
197M ASP* 4.1 1.6 - - + +
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Residues in contact with VAL 184 (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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107M ALA* 4.0 14.9 + - + +
110M LEU* 3.6 26.5 - - + -
124M TRP* 4.4 10.5 - - + -
136M TYR* 3.6 38.2 - - + -
137M ASP 3.3 4.9 - - - +
138M LEU* 3.8 25.1 - - + -
183M LEU* 1.3 82.2 - - - +
185M ARG* 1.3 60.0 + - - +
194M PRO 4.6 0.2 - - - +
195M CYS* 3.1 7.3 - - - -
196M THR* 2.9 38.9 + - - +
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Residues in contact with ARG 185 (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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136M TYR* 3.2 9.2 - - - -
137M ASP* 2.9 35.9 + - + +
139M TYR* 3.2 39.3 + - + -
148M GLN* 4.3 18.6 + - - +
183M LEU* 3.5 36.9 - - + +
184M VAL* 1.3 77.4 - - - +
186M GLY* 1.3 62.7 + - - +
187M ARG* 5.5 2.5 - - + -
193M ILE 5.7 0.9 - - - +
195M CYS* 3.9 11.4 - - + -
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Residues in contact with GLY 186 (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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134M VAL* 4.3 0.4 - - - -
135M GLN 3.5 5.8 - - - -
136M TYR* 3.8 11.9 - - - -
185M ARG* 1.3 78.6 - - - +
187M ARG* 1.3 66.0 + - - +
192M GLY* 5.4 0.3 - - - -
193M ILE* 3.8 42.8 + - - +
194M PRO 4.5 2.4 + - - -
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Residues in contact with ARG 187 (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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133M ASP 3.9 1.4 - - - +
134M VAL* 2.9 27.2 - - - +
135M GLN* 2.9 53.4 + - - +
137M ASP* 2.8 33.4 + - + +
162M ARG* 3.6 14.6 - - - +
185M ARG* 5.5 2.9 - - + +
186M GLY* 1.3 78.3 - - - +
188M SER* 1.3 61.0 + - - +
193M ILE* 4.4 0.7 - - - -
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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