Contacts of the strand formed by residues 74 - 81 (chain A) in PDB entry 1PF5
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 ILE 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.3 6.5 - - + -
64A LEU* 4.1 11.4 - - + -
71A PHE* 3.2 46.1 + - + +
72A ASP 4.5 4.0 - - - +
73A ASP* 1.3 77.4 - - - +
75A ILE* 1.3 64.1 + - - +
76A ASP 3.7 9.9 - - - +
77A VAL* 3.4 30.1 - - + -
99A PHE* 4.4 12.3 - - + -
105A PRO* 4.7 15.3 - - + +
122A ILE* 6.1 0.7 - - + -
124A VAL* 3.7 28.9 - - + -
125A ILE 3.6 4.3 - - - -
126A ALA* 4.2 2.7 - - + +
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Residues in contact with ILE 75 (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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30A LEU* 3.6 31.6 - - + -
73A ASP 3.3 1.1 + - - +
74A ILE* 1.3 79.5 - - - +
76A ASP* 1.3 62.5 + - + +
77A VAL* 5.7 0.2 - - - -
105A PRO* 6.1 0.7 - - - -
106A ASN* 3.4 16.5 + - - -
125A ILE* 2.7 27.8 + - + +
126A ALA* 4.2 0.7 - - - -
127A ARG* 3.6 37.2 - - + +
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Residues in contact with ASP 76 (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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74A ILE* 3.6 1.9 - - - +
75A ILE* 1.3 82.9 - - + +
77A VAL* 1.3 72.7 + - - +
78A THR* 4.0 12.5 + - - -
106A ASN* 2.9 26.2 + - - +
108A THR* 5.4 2.6 + - - -
123A LYS* 4.6 2.0 + - - +
124A VAL* 3.4 7.3 - - - +
125A ILE* 3.1 55.2 + - + +
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Residues in contact with VAL 77 (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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74A ILE* 3.4 31.4 - - + -
76A ASP* 1.3 76.2 - - - +
78A THR* 1.3 67.6 + - - +
99A PHE* 5.4 2.0 - - + -
105A PRO* 4.0 12.8 - - + -
106A ASN* 2.9 27.1 + - - +
107A TRP* 3.5 37.4 - - + +
108A THR* 3.0 24.1 + - - -
122A ILE* 3.8 23.6 - - + -
123A LYS 3.7 2.2 - - - -
124A VAL* 3.9 5.6 - - + -
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Residues in contact with THR 78 (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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76A ASP* 4.0 11.6 + - - -
77A VAL* 1.3 79.1 + - - +
79A SER* 1.3 62.5 + - - +
80A PHE* 3.6 28.2 - - + -
108A THR* 3.2 24.8 + - + +
110A VAL* 5.4 3.4 - - + -
121A GLU 4.1 0.2 - - - +
122A ILE* 3.5 2.1 - - - +
123A LYS* 2.7 54.4 + - + +
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Residues in contact with SER 79 (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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78A THR* 1.3 74.6 - - - +
80A PHE* 1.3 66.1 + - - +
81A HIS* 3.0 29.4 + - - -
107A TRP* 2.7 37.5 + - - +
108A THR 2.8 11.0 + - - +
109A ALA* 3.4 5.0 - - - +
110A VAL* 2.9 26.9 + - - +
120A PHE* 4.5 5.8 - - - -
121A GLU 3.2 10.1 - - - -
122A ILE* 4.7 4.3 - - - -
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Residues in contact with PHE 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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78A THR* 3.6 29.4 - - + -
79A SER* 1.3 75.2 - - - +
81A HIS* 1.3 71.6 + - - +
110A VAL* 3.3 13.7 - - + -
112A VAL* 3.6 22.4 - - + -
115A LEU* 3.7 25.4 - - + +
120A PHE* 3.5 3.5 - - - -
121A GLU* 2.9 49.7 + - + +
123A LYS* 4.0 31.2 - - + -
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Residues in contact with HIS 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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79A SER* 3.0 41.4 + - - -
80A PHE* 1.3 84.1 + - - +
82A THR* 1.3 59.7 + - - +
83A ASP 3.3 0.2 - - - -
84A PRO* 3.6 26.3 - - + +
87A GLN* 3.7 12.5 + - - +
91A ILE* 3.4 34.9 - - + +
109A ALA* 3.7 11.5 - - + +
110A VAL 2.9 24.9 + - - +
111A GLY* 3.4 5.2 - - - -
112A VAL* 2.8 32.6 + - - +
115A LEU* 4.6 0.2 - - - -
119A ASP 3.9 4.6 + - - -
120A PHE* 3.7 12.3 - + - -
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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