Contacts of the strand formed by residues 79 - 84 (chain A) in PDB entry 1PH0
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 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A MET* 2.9 34.1 + - - +
77A ALA* 3.2 12.8 - - + +
78A GLN* 1.3 81.4 + - - +
80A SER* 1.3 68.2 + - - +
81A TYR* 3.2 27.1 - - + +
199A ARG* 3.9 10.5 - - - +
204A LEU* 3.5 44.6 + - + +
205A SER* 4.8 5.9 + - - +
206A PRO* 5.6 2.2 - - - +
229A ASP* 2.8 48.2 + - - -
230A THR* 4.8 0.2 - - - +
233A LEU* 3.7 32.2 - - + +
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Residues in contact with SER 80 (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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71A LEU* 4.1 14.6 - - - -
72A ILE 3.3 7.2 - - - -
73A LYS* 3.6 27.5 + - - +
74A MET 4.7 0.2 + - - -
79A ARG* 1.3 80.3 + - - +
81A TYR* 1.3 72.6 + - - +
204A LEU* 5.3 4.1 + - - +
210A PRO* 4.0 23.5 - - - +
211A VAL* 4.0 4.5 + - - +
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Residues in contact with TYR 81 (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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70A SER 3.6 0.9 - - - +
71A LEU* 3.6 2.6 - - - +
72A ILE* 2.8 48.0 + - + +
74A MET* 4.2 7.4 - - + -
79A ARG* 3.2 23.9 - - + -
80A SER* 1.3 78.7 - - - +
82A ILE* 1.3 63.6 + - - +
83A LEU* 3.9 5.6 + - + -
204A LEU* 4.3 7.4 - - + -
210A PRO* 4.2 1.6 - - - -
211A VAL* 3.7 25.6 - - + -
213A VAL* 4.6 2.2 - - + -
225A PHE* 5.0 2.9 - + - -
226A CYS* 3.6 47.3 - - + -
229A ASP* 2.7 30.9 + - + -
230A THR* 2.7 33.3 + - - -
253A MET* 4.2 5.6 - - + -
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Residues in contact with ILE 82 (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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57A ILE* 3.8 31.9 - - + -
69A ALA* 4.0 7.2 - - + -
70A SER 3.2 8.3 - - - +
71A LEU* 4.3 3.1 - - + -
81A TYR* 1.3 74.5 - - - +
83A LEU* 1.3 62.1 + - - +
84A THR 4.0 0.2 + - - -
98A MET* 3.9 23.8 - - + -
102A GLN* 3.8 35.4 - - + +
104A SER* 4.6 2.7 - - - +
210A PRO* 3.6 29.8 - - + +
211A VAL 2.8 11.2 + - - +
212A VAL* 3.5 9.4 - - + +
213A VAL* 2.8 29.5 + - - +
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Residues in contact with LEU 83 (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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69A ALA* 3.2 2.4 - - - -
70A SER 2.8 31.1 + - - -
72A ILE* 4.2 15.0 - - + -
81A TYR* 3.9 8.7 - - + -
82A ILE* 1.3 79.0 - - - +
84A THR* 1.3 58.8 + - - +
213A VAL* 3.4 6.7 - - + +
218A GLY 3.7 12.3 - - - +
222A SER* 4.0 26.5 - - - +
223A GLY* 4.3 1.3 - - - +
226A CYS* 3.2 32.1 - - + -
257A ARG* 3.7 21.2 + - - -
260A LEU* 3.3 36.1 - - + -
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Residues in contact with THR 84 (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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67A ILE* 4.7 6.4 - - - +
68A ASN 2.7 21.5 + - - -
69A ALA* 3.4 14.9 - - - +
83A LEU* 1.3 74.6 - - - +
85A GLN* 1.3 74.0 + - - +
95A PHE* 3.6 24.4 - - + -
98A MET* 4.2 7.7 - - + +
212A VAL* 3.9 10.5 - - + -
213A VAL 3.0 9.6 + - - +
214A HIS* 3.1 31.4 - - + +
218A GLY* 3.2 17.9 + - - -
257A ARG* 4.2 3.4 - - - +
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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