Contacts of the strand formed by residues 77 - 82 (chain A) in PDB entry 5IFE
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 TYR 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A PHE* 4.0 0.2 - - - -
67A ALA* 3.3 25.5 - - - +
68A PHE* 3.1 49.3 + + + -
69A ARG* 5.0 0.9 - - - -
70A LEU* 4.8 16.0 - - + +
75A LYS* 3.9 19.7 - - + -
76A ASP* 1.3 74.8 - - - +
78A ILE* 1.3 66.7 + - - +
79A VAL 4.2 0.9 - - - -
89A ILE* 3.9 4.9 - - + -
90A LEU 3.5 14.6 - - - +
91A GLU* 3.9 33.9 + - + +
102A ILE* 4.4 6.5 - - + -
150A ALA 4.4 8.1 + - - -
151A ARG* 5.2 0.3 - - - -
152A LEU* 4.0 39.7 + - + +
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Residues in contact with ILE 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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18A ILE* 4.5 3.6 - - + -
22A PHE* 3.6 22.2 - - + -
31A VAL* 3.6 31.2 - - + -
38A LEU* 4.7 5.4 - - + -
65A LEU* 3.6 30.7 - - + -
66A MET 3.6 4.7 - - - +
76A ASP 4.7 0.7 - - - +
77A TYR* 1.3 79.1 - - - +
79A VAL* 1.3 61.5 - - - +
80A VAL* 3.7 11.0 + - + +
88A VAL 3.6 1.7 - - - +
89A ILE* 3.5 1.7 - - - -
90A LEU* 2.9 45.7 + - + +
92A TYR 5.2 5.2 - - - +
99A PHE* 3.8 27.6 - - + -
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Residues in contact with VAL 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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65A LEU* 3.8 2.1 - - - +
66A MET* 2.9 39.0 + - + +
68A PHE* 3.4 36.1 - - + -
78A ILE* 1.3 71.1 - - - +
80A VAL* 1.3 64.1 + - - +
87A ILE* 3.7 31.9 - - + -
88A VAL 3.4 5.8 - - - +
89A ILE* 3.9 13.2 - - + -
121A LEU* 3.3 25.7 - - + +
123A VAL* 5.7 1.8 - - + -
130A VAL* 4.0 13.7 - - + -
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Residues in contact with VAL 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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38A LEU* 4.6 6.5 - - + -
62A ILE* 4.2 22.0 - - + -
64A SER 3.7 8.7 - - - +
65A LEU* 3.7 9.0 - - + -
78A ILE* 3.7 25.4 - - + +
79A VAL* 1.3 79.8 - - - +
81A GLY* 1.3 65.7 + - - +
82A SER* 3.7 2.5 + - - -
86A ARG 4.6 0.7 - - - +
87A ILE* 4.2 5.5 - - - -
88A VAL* 2.9 41.8 + - + +
90A LEU* 4.5 11.9 - - + -
121A LEU* 4.3 1.3 - - - -
1156A CYS* 3.7 24.5 - - + -
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Residues in contact with GLY 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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62A ILE* 3.9 2.1 - - - -
63A ARG 2.9 24.3 + - - -
64A SER* 2.9 33.5 + - - +
80A VAL* 1.3 71.5 - - - +
82A SER* 1.3 58.9 + - - -
86A ARG 5.3 0.2 - - - -
118A GLY 3.5 10.9 - - - +
121A LEU* 3.8 4.7 - - - +
132A ILE* 4.4 17.5 - - - -
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Residues in contact with SER 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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60A GLY* 4.7 2.4 - - - -
61A VAL 3.4 14.7 + - - -
62A ILE* 4.5 1.3 - - - +
63A ARG* 3.7 16.9 + - - -
80A VAL* 3.7 5.2 + - - -
81A GLY* 1.3 74.8 - - - -
83A ASP* 1.3 81.4 + - - +
84A SER* 3.2 20.1 + - - +
86A ARG 4.5 8.8 + - - -
88A VAL* 5.9 0.2 - - - -
118A GLY* 3.8 9.3 - - - -
1156A CYS* 3.8 37.7 + - - +
1158A ARG* 5.0 0.7 - - - +
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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