Contacts of the strand formed by residues 140 - 145 (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 LEU 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ILE* 4.3 31.2 - - + +
129A GLN* 3.6 44.2 + - + +
130A ALA 4.7 2.6 - - - +
138A LEU 3.8 3.4 + - - -
139A ARG* 1.3 86.6 + - - +
141A TYR* 1.3 62.4 + - - +
142A ASN 3.5 27.8 - - - +
143A TYR* 5.7 0.7 - - + -
152A LEU* 4.1 18.6 - - + -
153A ILE 3.6 2.9 - - - +
154A LEU* 3.3 27.6 - - + +
219A PHE* 4.8 3.4 - - + -
872D ILE* 4.1 16.9 - - + +
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Residues in contact with TYR 141 (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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101A PHE* 3.8 20.4 - + - -
102A ILE 4.9 1.6 + - - -
103A VAL* 3.4 34.3 - - + -
139A ARG* 3.6 26.5 - - + +
140A LEU* 1.3 72.0 - - - +
142A ASN* 1.3 62.8 + - - +
153A ILE* 2.8 25.2 + - + +
154A LEU 3.5 16.6 - - - -
155A GLU* 3.5 27.1 - - + +
156A TYR 4.7 0.5 + - - -
858D GLN* 5.2 1.4 + - - -
865D LEU* 4.0 25.4 - - + -
869D PHE* 3.7 43.8 - + + +
870D GLY 5.0 2.1 - - - +
872D ILE* 3.2 18.2 - - - +
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Residues in contact with ASN 142 (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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70A ARG 3.6 14.6 + - - -
72A PHE* 4.2 5.7 - - - -
140A LEU* 3.5 11.7 - - - +
141A TYR* 1.3 82.2 - - - +
143A TYR* 1.3 79.3 + - - +
153A ILE* 2.9 40.9 + - + +
869D PHE* 2.9 33.7 + - + -
870D GLY* 4.8 2.2 - - - -
871D THR 4.5 5.9 + - - +
872D ILE* 3.6 31.1 - - - +
873D LEU 4.8 0.5 + - - -
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Residues in contact with TYR 143 (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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72A PHE* 4.9 2.9 - - - +
126A ILE* 4.1 25.1 - - + -
140A LEU* 5.1 1.6 - - + -
142A ASN* 1.3 98.8 + - - +
144A PHE* 1.3 80.8 + - - +
145A TYR* 4.0 20.1 - + - -
150A ILE* 4.7 4.9 - - + -
151A TYR 3.3 14.6 - - - +
152A LEU* 4.1 17.0 - - + -
153A ILE* 4.5 3.1 - - - +
872D ILE* 4.5 3.1 - - + -
873D LEU* 3.2 42.1 + - + +
874D PRO 3.3 13.2 + - - -
875D LEU* 3.5 32.8 - - + +
876D ASP 4.5 1.0 + - - -
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Residues in contact with PHE 144 (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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72A PHE* 3.7 39.0 - - + +
73A THR* 3.4 7.4 - - - -
74A ILE* 3.2 37.5 - - + -
77A PHE* 3.7 24.0 - + - -
105A LEU* 4.3 3.1 - - + -
143A TYR* 1.3 86.9 - - - +
145A TYR* 1.3 68.9 + - - +
150A ILE* 3.7 2.3 - - - +
151A TYR* 2.7 76.9 + + + +
153A ILE* 4.1 14.6 - - + -
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Residues in contact with TYR 145 (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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72A PHE 5.7 0.5 - - - +
110A LYS* 4.8 4.9 - - - -
143A TYR* 4.0 23.3 - + - -
144A PHE* 1.3 85.9 - - - +
146A ASP* 1.3 69.1 - - - +
149A ARG 3.2 15.3 - - - +
150A ILE* 3.7 16.2 - - + -
151A TYR* 4.2 5.6 - - - -
876D ASP* 4.7 6.7 - - - +
879D ASP* 3.4 36.3 + - - +
880D ILE* 3.5 32.5 - - + +
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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