Contacts of the strand formed by residues 184 - 187 (chain A) in PDB entry 2ADS
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 ARG 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ARG 4.0 1.8 + - - -
183A ILE* 1.3 80.4 - - + +
185A VAL* 1.3 64.4 + - - +
193A VAL* 4.0 2.7 - - + -
194A GLY 3.5 6.3 - - - -
195A ARG* 4.1 2.7 - - - +
257A PRO* 3.7 2.1 - - - +
258A VAL* 2.7 53.5 + - + +
259A LEU* 2.8 38.8 + - - +
260A THR* 3.2 23.8 - - - +
9G C 4.5 2.2 + - - +
10G C 2.7 58.3 + - - +
11G C 3.6 27.1 - - - +
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Residues in contact with VAL 185 (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* 4.4 19.7 - - + -
180A PRO* 5.4 1.6 - - + +
183A ILE* 4.1 4.5 - - + +
184A ARG* 1.3 78.6 - - - +
186A LYS* 1.3 63.9 + - - +
187A PRO* 4.6 0.9 - - - +
192A PHE 4.4 0.2 - - - +
193A VAL* 3.5 2.4 - - - +
194A GLY 3.0 27.4 + - - +
196A VAL* 3.5 22.9 - - + -
244A LEU* 3.4 35.5 - - + +
255A LEU* 4.5 17.7 - - + -
256A LYS 3.5 10.1 - - - +
257A PRO* 4.2 11.4 - - + -
258A VAL* 3.7 2.7 - - - -
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Residues in contact with LYS 186 (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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138A ILE* 3.9 13.5 - - - +
164A GLN* 2.8 55.5 + - + +
165A PRO* 4.4 16.7 + - + +
166A PHE* 5.3 3.6 - - - -
185A VAL* 1.3 77.0 - - - +
187A PRO* 1.3 79.1 - - + +
188A ILE* 3.5 8.4 + - - -
190A ILE 2.9 23.9 + - - +
191A ASP* 3.8 4.6 - - - +
192A PHE 3.8 6.3 - - - +
193A VAL* 3.9 8.7 - - + -
255A LEU* 4.2 2.0 - - - -
256A LYS* 2.9 31.7 + - - +
258A VAL* 3.3 18.2 - - + -
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Residues in contact with PRO 187 (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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185A VAL 4.6 0.9 - - - +
186A LYS* 1.3 90.3 - - + +
188A ILE* 1.3 68.7 + - - +
189A GLY 4.6 0.2 - - - +
190A ILE* 3.0 52.2 - - + +
192A PHE* 3.5 20.9 - - + +
244A LEU* 5.4 5.6 - - + -
250A TYR* 4.6 12.8 - - + -
254A ILE* 3.4 20.6 - - + +
255A LEU* 3.4 23.3 - - + -
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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