Contacts of the strand formed by residues 81 - 85 (chain A) in PDB entry 1P4J
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 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLN 5.2 0.4 + - - -
74A TYR* 2.9 49.7 + - - +
75A TYR* 3.8 11.7 + - - +
78A ASP* 3.9 16.4 + - - -
79A PRO* 3.7 14.6 + - - +
80A LYS* 1.3 72.5 - - - +
82A ILE* 1.3 60.1 + - - +
83A TYR* 3.7 30.9 - - + +
153A ALA* 3.5 11.9 - - - +
155A TYR* 2.8 40.7 + - + -
310A ARG* 4.5 16.6 - - + +
314A SER* 5.7 0.8 + - - +
332A LYS* 2.9 16.3 + - + +
333A VAL* 3.6 2.2 - - + -
334A ALA* 3.0 27.7 + - - +
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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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80A LYS* 4.5 5.6 - - + +
81A ARG* 1.3 75.0 - - - +
83A TYR* 1.3 69.1 + - - +
84A TYR* 4.0 2.8 + - + +
147A MET* 4.7 3.6 - - - -
152A LEU* 4.9 7.2 - - + -
153A ALA 3.0 13.4 + - - +
154A ALA* 3.3 16.2 - - + +
155A TYR* 2.8 29.6 + - - +
334A ALA* 3.7 15.0 - - + +
336A GLN* 5.6 1.3 - - + -
825A TRP* 3.5 71.8 - - + +
827A VAL* 4.3 20.0 - - + -
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Residues in contact with TYR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 3.7 28.9 - - + +
82A ILE* 1.3 75.3 - - - +
84A TYR* 1.3 62.3 + - - +
85A LEU* 3.6 11.7 + - + +
155A TYR* 3.5 22.4 - + + +
157A TYR* 3.4 24.9 - + + -
307A ILE* 3.6 44.3 + - + -
310A ARG* 3.1 49.9 + - - +
333A VAL* 3.8 17.2 - - + +
334A ALA 2.8 19.9 + - - +
335A ILE* 3.4 3.7 - - + -
336A GLN 2.9 26.7 + - - -
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Residues in contact with TYR 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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82A ILE* 4.0 2.5 + - + -
83A TYR* 1.3 70.7 - - - +
85A LEU* 1.3 61.6 + - - +
86A SER* 3.8 2.6 + - - -
89A PHE* 3.8 16.7 - + - -
139A LEU* 4.6 3.6 - - - +
140A ALA* 3.7 27.7 - - + -
143A PHE* 3.5 36.1 - + - -
144A LEU* 4.6 4.3 - - + -
147A MET* 4.5 22.9 - - + -
154A ALA* 6.3 0.2 - - + -
155A TYR 3.0 14.3 + - - +
156A GLY* 3.7 3.8 - - - -
157A TYR 3.1 24.7 + - - +
336A GLN* 3.8 32.1 - - + -
338A ASN* 3.1 37.9 + - + -
375A THR* 5.8 2.5 + - - +
377A HIS* 5.0 0.3 - - - -
820A TYR* 5.8 1.3 - + - -
825A TRP* 4.8 10.3 - + - -
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Residues in contact with LEU 85 (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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83A TYR* 3.8 22.7 - - + +
84A TYR* 1.3 72.2 - - - +
86A SER* 1.3 61.0 + - - +
157A TYR* 3.8 10.1 - - + +
299A VAL* 5.5 4.5 - - + -
300A VAL* 4.4 10.8 - - + +
303A THR* 3.8 35.2 - - + +
304A LEU* 5.5 4.3 - - + -
307A ILE* 4.9 0.9 - - + -
335A ILE* 3.9 21.8 - - + -
336A GLN 3.0 13.4 + - - +
337A LEU* 4.7 0.9 - - + -
338A ASN* 3.1 29.1 + - - +
342A PRO* 3.8 27.9 - - + +
345A ALA* 4.3 15.0 - - + -
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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