Contacts of the strand formed by residues 180 - 184 (chain A) in PDB entry 4MNY
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 MET 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ALA* 4.8 0.2 - - + -
99A HIS 3.3 24.7 - - - +
100A HIS* 3.5 28.3 - - + +
165A HIS* 4.9 6.1 - - - +
175A GLU 3.5 21.1 - - - +
176A VAL* 3.8 7.4 - - + -
177A THR* 3.0 31.8 + - - +
178A THR* 4.1 5.7 - - - +
179A LYS* 1.3 83.9 - - - +
181A LEU* 1.3 69.3 - - - +
182A CYS* 5.8 0.9 - - - -
215A TRP* 3.6 21.1 - - + +
227A VAL* 3.7 13.0 - - + -
228A TYR 3.2 11.9 - - - +
229A THR* 5.4 1.8 - - - -
230A ARG* 4.1 1.7 + - - -
1005A GOL 3.5 10.3 - - - -
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Residues in contact with LEU 181 (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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130A PRO* 5.9 0.7 - - + -
162A LEU* 4.9 15.3 - - + -
163A ILE 5.8 2.9 - - - +
180A MET* 1.3 75.5 - - - +
182A CYS* 1.3 66.2 + - - +
199A LEU* 4.3 12.6 - - + -
210A THR* 3.5 43.7 - - + +
211A GLY* 4.9 0.7 - - - -
227A VAL* 3.4 2.8 - - - -
228A TYR* 2.7 49.9 + - + +
230A ARG* 3.7 43.5 - - + +
1006A GOL 5.7 8.1 - - - -
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Residues in contact with CYS 182 (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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162A LEU* 3.7 5.9 - - - +
163A ILE* 3.0 38.5 + - + +
165A HIS* 6.2 0.9 - - - -
168A CYS* 2.0 53.2 - - + -
172A TYR* 4.4 0.2 - - - -
176A VAL* 3.8 17.9 - - - -
180A MET 5.8 0.7 - - - -
181A LEU* 1.3 77.9 - - - +
183A ALA* 1.3 63.3 + - - +
225A PRO* 4.0 7.9 - - + -
226A GLY 3.3 4.0 - - - -
227A VAL* 4.4 11.0 - - - -
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Residues in contact with ALA 183 (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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160A VAL* 3.7 24.0 - - + +
161A LYS 3.2 17.0 - - - +
162A LEU* 4.2 12.3 - - + -
163A ILE* 4.1 3.1 - - - -
182A CYS* 1.3 78.0 - - - +
184A ALA* 1.3 62.1 + - - +
189A ASP* 4.4 2.8 - - - +
199A LEU* 4.6 3.1 - - + -
225A PRO* 4.1 0.2 - - - -
226A GLY* 2.9 33.3 + - - +
228A TYR* 3.9 15.3 + - + -
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Residues in contact with ALA 184 (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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160A VAL* 3.9 10.2 - - - +
161A LYS* 2.9 32.2 + - - +
163A ILE* 3.7 15.6 - - + +
183A ALA* 1.3 77.6 - - - +
185A ASP* 1.3 68.3 + - - +
186A TRP* 3.5 34.8 - - + -
188A THR 5.1 1.6 - - - +
189A ASP* 5.3 4.9 - - - +
225A PRO* 4.0 6.3 - - + -
226A GLY 4.7 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