Contacts of the strand formed by residues 181 - 185 (chain A) in PDB entry 5AN9
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ARG* 3.6 13.7 + - - -
26A GLN* 3.7 4.4 + - - +
87A VAL* 5.7 0.2 - - + -
117A ARG* 4.6 21.5 - - + +
121A ASN* 3.3 28.2 - - - +
164A ILE* 3.5 31.9 - - + -
165A ALA 3.5 7.9 - - - +
166A HIS* 3.9 11.7 - - + -
179A ALA 3.4 9.4 + - - +
180A HIS* 1.3 72.3 - - - +
182A LEU* 1.3 76.2 + - - +
3337N G 5.8 1.6 - - - +
3338N C 3.8 21.2 - - - +
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Residues in contact with LEU 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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24A ARG* 4.0 10.3 - - - +
26A GLN* 4.0 8.3 - - + -
27A GLY 3.7 18.2 - - - +
28A LYS* 4.7 3.8 - - + -
47A MET* 3.4 29.3 - - + +
84A MET* 4.8 3.0 - - + +
164A ILE* 5.0 0.2 - - - -
165A ALA* 3.0 32.0 + - - +
180A HIS 4.1 1.4 + - - -
181A VAL* 1.3 81.8 - - - +
183A GLU* 1.3 67.3 + - - +
184A ILE* 3.5 8.7 + - + +
345A THR* 3.1 39.0 - - + +
347A ARG* 5.5 5.8 - - - +
3338N C 4.4 0.7 - - - -
3339N G 3.5 21.3 - - - +
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Residues in contact with GLU 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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32A PHE* 3.4 19.2 - - + -
45A ALA* 5.3 0.3 - - - +
90A VAL* 3.3 30.1 - - + +
92A TYR* 6.1 0.7 - - - -
101A THR* 5.4 0.7 + - - -
162A ARG* 3.8 28.0 + - + -
163A VAL 3.5 7.6 - - - +
164A ILE* 4.2 15.0 - - + +
182A LEU* 1.3 76.0 - - - +
184A ILE* 1.3 63.4 + - - +
185A GLN 4.0 0.4 - - - -
347A ARG* 5.0 2.4 + - - -
3338N C 3.0 30.9 + - - +
3339N G 2.7 51.1 + - - +
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Residues in contact with ILE 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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32A PHE* 4.2 4.3 - - - -
43A LEU* 3.6 42.0 - - + +
45A ALA* 3.5 34.3 - - + +
46A PHE* 4.3 6.1 - - + +
84A MET* 5.2 7.9 - - + -
86A ILE* 4.0 6.7 - - + -
162A ARG* 4.3 0.7 - - - -
163A VAL* 3.1 40.5 + - + +
165A ALA* 3.9 19.7 - - + -
182A LEU* 4.0 11.4 - - + +
183A GLU* 1.3 77.5 - - - +
185A GLN* 1.3 65.2 + - - +
186A VAL* 4.2 0.2 - - - +
206A VAL* 4.9 3.8 - - + -
345A THR* 5.9 0.9 - - - +
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Residues in contact with GLN 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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32A PHE* 3.4 43.9 + - + +
33A PRO 3.6 15.1 + - - +
35A ASP* 4.4 5.7 + - - +
43A LEU 3.1 4.4 + - - +
44A THR* 2.5 32.6 + - - +
92A TYR* 5.8 1.2 - - - -
160A VAL* 3.8 31.5 - - + +
161A VAL 3.9 0.4 - - - +
162A ARG* 3.7 37.4 + - + +
183A GLU 4.0 0.6 - - - -
184A ILE* 1.3 70.7 - - - +
186A VAL* 1.3 56.7 + - - +
187A ASN* 2.6 27.5 + - - -
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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