Contacts of the strand formed by residues 75 - 81 (chain A) in PDB entry 1F5F
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 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A LEU* 3.3 4.2 - - - -
72A ARG* 2.9 29.8 + - - +
73A ASP* 3.9 8.5 + - - +
74A GLY* 1.3 79.8 - - - +
76A PRO* 1.3 79.8 - - + +
77A GLU* 4.5 0.3 - - - +
90A GLY* 5.8 1.6 - - - -
91A ALA* 4.2 5.6 - - - +
92A GLY 3.0 27.0 + - - +
93A PRO* 3.7 11.4 - - - +
94A ARG* 3.8 32.6 - - + +
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Residues in contact with PRO 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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69A LEU* 4.4 7.2 - - + -
70A GLY 3.2 10.3 - - - +
71A LEU* 3.6 3.9 - - + -
75A ARG* 1.3 87.1 - - - +
77A GLU* 1.3 56.4 + - - +
78A ILE* 5.9 0.2 - - - -
90A GLY* 3.3 4.2 - - - -
91A ALA* 3.0 44.1 + - + +
92A GLY* 4.6 1.1 - - - -
93A PRO 3.2 17.9 - - - +
95A LEU* 4.0 23.3 - - + -
114A LEU* 3.8 27.6 - - + -
116A VAL* 4.5 11.2 - - + -
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Residues in contact with GLU 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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68A MET* 3.7 8.3 - - + +
69A LEU* 3.5 4.3 - - - +
70A GLY 2.8 40.2 + - - +
71A LEU 4.9 0.7 - - - +
72A ARG* 2.6 52.2 + - + +
75A ARG 3.5 0.4 + - - +
76A PRO* 1.3 73.3 - - - +
78A ILE* 1.3 75.4 - - - +
79A GLN* 2.8 30.1 + - + +
88A THR* 4.0 12.3 - - - +
89A VAL 3.3 16.8 - - - +
90A GLY* 4.7 3.2 + - - -
155A LEU* 4.4 1.2 - - - +
157A LEU* 4.4 2.6 - - - +
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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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67A PHE* 3.7 40.8 - - + -
68A MET 3.2 3.1 - - - +
69A LEU* 3.8 17.7 - - + -
77A GLU* 1.3 78.7 - - - +
79A GLN* 1.3 72.5 + - - +
80A LEU* 4.3 1.1 - - + -
87A LEU* 3.8 4.7 - - + +
88A THR* 3.4 2.8 - - - -
89A VAL* 2.8 39.2 + - + +
105A VAL* 5.2 1.3 - - + -
112A VAL* 4.9 6.7 - - + -
114A LEU* 4.4 20.0 - - + -
122A LEU* 4.0 23.8 - - + -
124A LEU* 3.8 24.7 - - + -
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Residues in contact with GLN 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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66A TRP* 3.7 16.6 - - + -
67A PHE* 3.4 2.3 - - - -
68A MET* 2.7 52.4 + - + +
72A ARG* 3.6 1.8 - - - +
77A GLU* 2.8 27.0 + - - +
78A ILE* 1.3 79.8 - - - +
80A LEU* 1.3 65.3 - - - +
87A LEU 3.2 4.7 - - - +
88A THR* 3.9 16.4 - - + +
153A LEU* 3.5 11.1 - - - +
154A ARG* 3.0 31.3 + - - +
155A LEU* 2.9 30.3 + - - +
157A LEU* 5.0 0.2 - - - +
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Residues in contact with LEU 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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66A TRP* 3.5 6.3 - - - -
67A PHE* 4.1 19.1 - - + +
78A ILE* 4.3 2.2 - - + -
79A GLN* 1.3 79.8 - - - +
81A HIS* 1.3 63.2 + - - +
82A ASN* 4.0 14.8 - - - +
85A ALA* 3.6 37.0 - - + +
86A GLN* 3.3 2.6 - - - -
87A LEU* 2.9 44.4 + - + +
112A VAL* 4.6 3.1 - - + -
124A LEU* 4.1 17.0 - - + -
127A VAL* 4.0 25.8 - - + -
154A ARG* 3.8 3.0 - - - -
253A DHT 4.4 17.5 - - + -
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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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63A LYS 4.1 11.9 + - - -
64A ASP* 3.3 25.9 + - - +
65A ASP* 3.1 3.6 - - - -
66A TRP* 2.8 66.8 + - + +
80A LEU* 1.3 75.5 - - - +
82A ASN* 1.3 67.3 + - - +
85A ALA 3.5 4.3 - - - -
86A GLN* 3.6 23.5 - - + +
154A ARG* 4.8 8.7 + - - +
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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