Contacts of the strand formed by residues 176 - 181 (chain M) in PDB entry 6CNC
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 VAL 176 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B THR* 5.6 4.8 + - - -
543B LEU* 4.1 24.9 - - + -
87M VAL* 3.5 28.7 - - + +
89M GLN* 5.4 7.9 - - + -
152M GLY* 2.8 1.7 - - - -
153M VAL* 2.6 45.6 + - - +
155M ASN* 4.6 2.7 - - - +
158M GLN* 4.6 13.2 - - - +
173M ILE* 3.6 21.3 - - + -
174M GLU 3.2 15.7 - - - +
175M ARG* 1.3 73.5 - - - +
177M ALA* 1.3 67.8 + - - +
178M GLN* 6.0 1.1 - - - +
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Residues in contact with ALA 177 (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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87M VAL 3.8 8.5 + - - +
88M PHE* 4.0 13.8 - - + -
89M GLN* 3.6 20.1 + - - +
117M HIS* 3.5 22.9 - - + +
119M TRP* 5.9 1.3 - - + -
150M GLY 4.4 0.9 - - - +
151M VAL 3.7 2.5 - - - +
152M GLY* 3.4 18.4 - - - -
175M ARG 4.2 0.8 + - - -
176M VAL* 1.3 80.0 - - - +
178M GLN* 1.3 75.1 + - - +
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Residues in contact with GLN 178 (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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343B ARG* 4.4 26.5 - - - +
542B THR* 2.4 39.5 + - - +
543B LEU* 4.1 0.4 - - - +
544B ILE 4.4 2.1 + - - -
545B ASP* 4.4 3.9 - - - +
88M PHE* 5.9 0.5 - - - -
89M GLN* 2.9 43.6 + - - +
91M ALA 5.3 0.2 + - - -
150M GLY* 3.6 12.8 + - - -
151M VAL 3.8 9.0 + - - +
176M VAL* 6.0 1.8 - - - +
177M ALA* 1.3 89.5 - - - +
179M LEU* 1.3 65.5 + - - +
180M LYS* 4.3 14.4 - - + -
392N GLN* 3.9 9.7 + - - -
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Residues in contact with LEU 179 (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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88M PHE* 4.9 15.3 - - + -
89M GLN 3.5 7.0 + - - -
90M TYR* 3.3 27.3 - - + +
91M ALA* 3.5 20.6 + - - +
119M TRP* 3.8 3.1 - - + +
121M ILE* 3.6 32.8 - - + -
148M LEU* 3.4 59.3 - - + +
149M LYS* 3.4 12.8 - - - +
150M GLY 3.9 1.3 - - - +
178M GLN* 1.3 78.0 + - - +
180M LYS* 1.3 61.5 + - - +
181M PRO* 3.9 5.4 - - - +
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Residues in contact with LYS 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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261B GLY 2.4 43.8 + - - +
262B ILE* 3.2 26.8 - - + +
263B LEU* 4.3 14.4 - - + +
264B SER* 5.7 4.9 - - - +
343B ARG* 4.2 24.6 - - - +
91M ALA* 6.4 1.6 - - + -
148M LEU* 4.3 1.3 - - - -
149M LYS 2.8 39.3 + - - +
150M GLY* 4.6 1.5 - - - -
178M GLN* 5.0 12.8 - - + -
179M LEU* 1.3 77.9 - - - +
181M PRO* 1.3 73.5 - - + +
182M PHE* 3.8 5.4 - - - -
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Residues in contact with PRO 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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263B LEU* 3.2 22.2 - - - +
264B SER* 5.9 9.2 - - - -
296B TYR* 5.1 0.4 - - - -
8I CYS* 4.3 16.6 - - - +
9I ASN* 5.8 1.1 - - + +
91M ALA 4.5 4.9 - - - +
92M ASN* 3.7 24.9 - - - +
146M GLN* 4.0 13.5 - - - +
147M THR 3.2 11.0 - - - +
148M LEU* 3.6 24.4 - - + -
179M LEU 3.9 7.0 - - - +
180M LYS* 1.3 89.8 - - + +
182M PHE* 1.3 60.1 + - - +
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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