Contacts of the strand formed by residues 206 - 211 (chain A) in PDB entry 1P84
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 ALA 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 5.3 6.4 - - + +
37A VAL* 3.2 15.4 + - - +
53A VAL* 3.9 7.9 - - + -
54A VAL 3.6 6.3 - - - -
55A PHE* 3.6 17.9 - - + -
202A LEU 3.3 17.9 - - - +
203A ASN* 3.0 15.9 + - - +
204A SER 3.5 2.0 - - - +
205A ASN* 1.3 81.2 - - - +
207A VAL* 1.3 73.2 + - - +
395A LEU* 4.4 3.1 - - - +
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Residues in contact with VAL 207 (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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36A ILE* 5.4 0.7 - - - -
37A VAL* 3.5 29.2 - - + +
39A ALA* 4.1 7.6 - - + -
53A VAL* 3.3 3.2 - - - -
54A VAL* 2.8 39.9 + - + +
206A ALA* 1.3 85.4 - - - +
208A VAL* 1.3 65.7 + - - +
209A VAL* 3.6 18.7 + - + +
391A GLY* 4.5 0.7 - - - +
394A VAL* 3.6 31.2 - - + +
395A LEU* 3.8 26.2 - - + -
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 3.8 19.1 - - + +
37A VAL 3.4 6.8 + - - +
38A VAL* 3.6 31.8 - - + +
39A ALA* 3.0 27.4 + - - +
51A VAL* 4.8 7.4 - - + -
52A GLY 3.4 13.7 - - - +
53A VAL* 4.1 7.4 - - + +
117A LEU* 5.1 4.0 - - + -
120A LEU* 6.5 1.3 - - + -
207A VAL* 1.3 71.7 - - - +
209A VAL* 1.3 65.5 + - - +
219A LEU* 4.6 5.4 - - + -
223A ILE* 3.7 24.0 - - + -
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA* 3.3 4.3 - - + +
50A SER 4.1 0.8 - - - +
51A VAL* 3.4 6.4 - - - +
52A GLY 2.6 38.1 + - - +
54A VAL* 3.6 20.2 - - + -
105A ILE* 6.4 0.7 - - + -
207A VAL* 3.8 11.2 - - + +
208A VAL* 1.3 77.6 - - - +
210A GLY* 1.3 62.0 + - - +
211A THR* 4.1 2.2 - - + -
219A LEU* 4.5 3.4 - - - -
387A ALA* 3.6 33.5 - - + +
390A LEU* 3.7 25.8 - - + -
391A GLY* 3.6 27.1 - - - -
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Residues in contact with GLY 210 (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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39A ALA 3.0 9.7 + - - -
40A THR* 3.1 36.3 - - - +
41A GLU 3.2 6.2 + - - +
50A SER 3.5 7.2 - - - -
51A VAL* 4.6 1.6 - - - -
209A VAL* 1.3 76.9 - - - +
211A THR* 1.3 61.9 + - - -
214A ILE* 4.1 10.9 - - - +
219A LEU* 4.0 9.9 - - - -
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Residues in contact with THR 211 (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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41A GLU* 3.8 15.0 - - + +
49A ALA* 3.6 3.5 - - - +
50A SER* 2.7 37.4 + - - +
209A VAL* 4.1 1.5 - - + +
210A GLY* 1.3 79.3 - - - +
212A GLY* 1.3 54.2 + - - +
213A ASN 4.0 1.6 - - - -
214A ILE* 4.6 5.0 - - - +
383A PRO* 2.9 29.6 + - - +
386A ASP* 3.9 13.9 - - + -
387A ALA* 3.7 25.7 + - - +
390A LEU* 3.8 23.8 - - + -
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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