Contacts of the strand formed by residues 109 - 114 (chain A) in PDB entry 1F7U
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 PHE 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LEU* 3.8 17.7 - - + -
71A ILE 3.3 6.1 - - - +
72A PRO* 3.6 25.6 - - + -
74A PRO* 6.3 0.2 - - + -
87A ALA* 3.4 6.3 - - - +
105A ALA* 3.4 4.3 - - - -
106A ASN* 2.9 38.5 + - - +
107A GLY 3.0 1.8 - - - -
108A PRO* 1.3 100.6 - - + +
110A ILE* 1.3 67.3 - - - +
918B G 3.4 41.3 - - - -
919B H2U 3.3 63.5 - + - +
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Residues in contact with ILE 110 (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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43A LEU* 4.7 7.4 - - + -
70A LEU* 3.2 5.0 - - - -
71A ILE* 3.1 36.8 + - + -
73A ILE* 3.8 23.3 - - + -
87A ALA* 3.8 21.3 - - + +
90A TRP* 3.8 33.4 - - + -
91A ALA* 4.3 4.5 - - + +
94A PHE* 5.7 0.7 - - + -
103A VAL* 3.5 23.1 - - + -
104A GLU 3.4 6.1 - - - +
109A PHE* 1.3 78.2 - - - +
111A GLN* 1.3 63.8 + - - +
112A PHE* 3.4 24.4 - - + -
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Residues in contact with GLN 111 (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 GLU 4.3 1.9 + - - +
66A ARG* 3.2 42.2 + - - +
69A LEU 3.8 3.6 - - - -
70A LEU* 4.2 4.9 - - + -
102A LYS 4.0 0.5 - - - +
103A VAL* 3.3 7.1 - - - +
104A GLU* 2.6 51.5 + - - +
106A ASN* 3.7 24.2 + - + +
110A ILE* 1.3 74.8 - - - +
112A PHE* 1.3 61.9 + - - +
113A PHE* 3.5 26.0 - - + -
919B H2U 2.8 33.9 + - - +
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Residues in contact with PHE 112 (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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39A ILE* 3.5 47.8 - - + -
43A LEU* 4.6 7.6 - - + -
58A LEU* 3.9 7.2 - - + -
68A ASP* 2.9 26.0 + - - +
69A LEU* 2.8 29.3 + - + +
71A ILE* 3.8 17.9 - - + -
94A PHE* 3.7 28.0 - + - -
100A LEU* 4.2 9.4 - - + -
102A LYS 4.0 2.5 - - - -
103A VAL* 3.8 21.5 - - + -
110A ILE* 3.4 38.1 - - + -
111A GLN* 1.3 73.3 - - - +
113A PHE* 1.3 62.4 + - - +
114A PHE* 4.0 2.3 - - + -
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Residues in contact with PHE 113 (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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64A MET 3.7 9.9 - - - -
65A GLU* 3.5 15.3 - - - -
66A ARG 3.7 1.1 - - - -
67A GLY* 3.2 33.9 - - - -
68A ASP* 3.7 2.9 - - - +
100A LEU* 3.4 7.1 - - - +
101A GLU* 2.8 32.0 + - + -
102A LYS* 2.9 63.0 + - + +
104A GLU* 4.1 9.0 - - + -
111A GLN* 3.5 28.5 - - + -
112A PHE* 1.3 73.5 - - - +
114A PHE* 1.3 65.6 + - - +
529A ARG* 4.4 15.3 - - - -
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Residues in contact with PHE 114 (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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31A ILE* 5.6 1.8 - - + -
32A VAL* 4.3 23.1 - - + -
35A MET* 3.4 52.7 - - + -
39A ILE* 4.2 9.4 - - + -
68A ASP* 2.8 40.2 + - + +
69A LEU* 3.5 32.5 - - + -
99A PHE 3.7 4.3 - - - -
100A LEU* 4.2 7.6 - - + +
101A GLU* 3.8 4.5 - - - +
112A PHE 4.6 3.1 - - - -
113A PHE* 1.3 78.1 - - - +
115A ASN* 1.3 60.8 + - - +
116A PRO* 3.1 17.0 - - - +
119A LEU* 3.8 28.7 - - + -
529A ARG* 5.4 1.4 - - - -
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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