Contacts of the strand formed by residues 102 - 109 (chain A) in PDB entry 4AF3
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.8 10.5 - - + -
94A ALA 3.4 9.9 - - - +
95A ARG* 4.1 14.1 - - + -
100A HIS 4.5 5.6 - - - +
101A PHE* 1.3 74.9 - - - +
103A VAL* 1.3 70.1 + - - +
141A TYR* 4.9 1.7 + - - -
156A TYR* 3.8 34.7 + - + +
845D TRP* 4.2 13.7 - - + +
851D LEU* 3.9 19.1 - - + -
854D ALA* 3.6 31.0 - - + -
855D ILE* 4.0 9.9 - - + -
858D GLN* 2.8 40.4 + - - +
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Residues in contact with VAL 103 (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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77A PHE* 4.0 26.0 - - + -
93A LEU* 3.9 2.4 - - - -
94A ALA* 2.9 43.9 + - + +
96A GLU* 6.2 0.7 - - + -
101A PHE* 3.6 17.9 + - + +
102A ILE* 1.3 82.2 - - - +
104A ALA* 1.3 65.0 + - - +
105A LEU* 4.6 2.5 - - + +
141A TYR* 3.4 32.3 - - + -
153A ILE* 3.7 15.5 - - + -
154A LEU 3.3 9.6 - - - +
156A TYR* 3.8 8.4 - - - +
869D PHE* 4.2 3.8 - - + -
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Residues in contact with ALA 104 (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 LEU* 4.3 6.7 - - + -
91A VAL* 4.7 0.9 - - + -
92A TYR 3.3 8.1 - - - +
93A LEU* 4.8 0.4 - - - +
103A VAL* 1.3 74.5 - - - +
105A LEU* 1.3 60.0 + - - +
153A ILE* 4.0 0.9 - - - -
154A LEU* 2.7 40.4 + - - +
155A GLU 3.8 6.5 - - - +
156A TYR* 3.9 5.9 - - + +
500A VX6 3.4 47.1 - - + +
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Residues in contact with LEU 105 (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* 3.8 29.2 - - + -
77A PHE* 4.4 21.3 - - + -
79A ILE* 4.4 13.0 - - + -
91A VAL* 3.3 3.1 - - - -
92A TYR* 2.7 52.9 + - + +
94A ALA* 4.4 9.9 - - + -
103A VAL* 4.1 1.5 - - + -
104A ALA* 1.3 73.7 - - - +
106A LYS* 1.3 59.8 + - - +
107A VAL* 5.4 3.1 - - + -
144A PHE* 4.3 11.0 - - + -
151A TYR* 4.5 14.1 - - + -
152A LEU 3.4 17.9 - - - +
153A ILE* 3.9 25.8 - - + -
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Residues in contact with LYS 106 (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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88A PHE* 2.5 32.1 + - - +
89A GLY* 4.6 4.5 - - - -
90A ASN 3.3 11.9 - - - +
91A VAL* 4.0 8.5 - - + -
104A ALA 4.1 0.8 + - - -
105A LEU* 1.3 72.6 - - - +
107A VAL* 1.3 67.0 + - - +
108A LEU* 3.8 24.0 + - + -
150A ILE 3.5 2.6 - - - +
151A TYR* 3.4 3.4 - - - -
152A LEU* 2.8 47.8 + - + +
154A LEU* 4.4 15.0 - - + +
219A PHE* 5.7 3.1 - - + +
500A VX6 3.4 42.1 + - + +
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Residues in contact with VAL 107 (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* 6.0 0.4 - - + -
90A ASN* 2.8 39.8 + - + +
92A TYR* 4.2 23.6 - - + -
105A LEU* 5.1 4.0 - - + +
106A LYS* 1.3 74.4 - - - +
108A LEU* 1.3 66.3 - - - +
109A PHE* 3.7 11.4 - - + -
149A ARG* 3.4 44.4 - - + -
150A ILE 3.6 2.2 - - - -
151A TYR* 3.5 26.9 - - + -
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Residues in contact with LEU 108 (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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106A LYS* 4.0 25.1 - - + +
107A VAL* 1.3 79.8 - - - +
109A PHE* 1.3 64.0 + - - +
110A LYS 3.6 0.9 + - - -
113A ILE* 4.2 13.9 - - + -
122A LEU* 3.8 25.6 - - + -
149A ARG* 3.3 2.5 - - - -
150A ILE* 2.6 55.6 + - + +
152A LEU* 3.7 31.4 - - + -
219A PHE* 5.6 2.0 - - + -
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Residues in contact with PHE 109 (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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90A ASN* 3.2 31.4 - - - +
107A VAL* 3.7 14.6 - - + -
108A LEU* 1.3 71.4 - - - +
110A LYS* 1.3 64.8 + - - +
111A SER* 4.0 12.1 - - - +
112A GLN* 2.9 38.9 + - + +
113A ILE* 3.2 12.3 + - - +
148A ARG* 3.8 13.5 - - + -
149A ARG* 3.8 28.5 - - + -
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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