Contacts of the strand formed by residues 142 - 150 (chain A) in PDB entry 4IYT
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A TRP* 3.7 5.4 - - - -
75A PRO 2.7 23.3 + - - -
76A PHE 3.6 8.7 - - - -
78A TYR* 4.3 6.5 - + - -
101A ASP* 4.2 9.9 - - - +
139A GLN* 2.9 27.5 + - - +
140A GLN 3.2 12.1 - - - -
141A ASN* 1.3 82.6 + - - +
143A ILE* 1.3 61.5 - - - +
158A ILE* 3.3 23.8 - - + -
159A LYS 3.1 19.1 - - - -
160A ALA* 3.4 20.2 - - + -
161A ASN* 3.9 5.0 + - - +
163A PHE* 4.2 9.4 - + - -
199A PRO* 4.2 3.6 - - + -
201A LEU* 3.6 39.9 + - + -
202A VAL* 3.3 27.9 - - + +
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Residues in contact with ILE 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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99A LYS* 3.7 37.2 - - + -
100A ILE 3.5 15.7 - - - +
101A ASP* 3.8 20.9 - - + +
139A GLN* 3.6 4.0 - - - -
142A TYR* 1.3 74.9 - - - +
144A SER* 1.3 61.6 + - - +
145A GLU* 5.7 2.7 - - + -
157A GLY 3.5 2.9 - - - +
158A ILE* 3.3 2.5 - - - -
159A LYS* 2.9 56.5 + - + +
161A ASN* 3.6 32.5 - - + +
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Residues in contact with SER 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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96A PRO* 4.7 5.2 - - - -
98A ASN 4.0 1.4 - - - +
99A LYS* 3.2 5.5 - - - +
100A ILE* 2.9 47.7 + - - -
137A TYR* 2.6 27.6 + - - -
139A GLN* 2.6 20.5 + - - -
143A ILE* 1.3 71.7 - - - +
145A GLU* 1.3 62.0 + - - +
156A TRP* 5.5 1.8 - - - -
157A GLY 3.5 4.7 - - - -
158A ILE* 3.5 16.6 - - - +
210A PHE* 5.3 1.6 - - - -
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Residues in contact with GLU 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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98A ASN 4.9 1.6 - - - -
99A LYS* 3.5 47.4 + - + +
143A ILE* 5.5 2.9 - - + +
144A SER* 1.3 74.3 - - - +
146A VAL* 1.3 74.5 + - - +
147A GLU* 3.4 0.7 + - - +
156A TRP* 3.5 7.9 - - - -
157A GLY* 2.9 33.4 + - - +
159A LYS* 5.9 3.1 - - - -
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Residues in contact with VAL 146 (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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94A TYR* 3.7 29.4 - - + +
96A PRO 4.0 0.7 - - - +
97A LYS 3.8 17.2 + - - +
145A GLU* 1.3 85.6 - - + +
147A GLU* 1.3 62.1 + - - +
148A HIS* 3.5 28.5 - - - +
149A GLN* 3.8 13.7 - - + +
154A VAL* 4.3 5.4 - - + -
155A GLN 3.5 4.9 - - - +
156A TRP* 3.7 22.4 - - + +
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Residues in contact with GLU 147 (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 GLN* 3.2 30.4 + - - +
79A ASN* 4.3 0.9 - - - +
145A GLU 3.4 1.8 + - - +
146A VAL* 1.3 72.7 - - - +
148A HIS* 1.3 60.8 - - + +
155A GLN* 2.7 41.0 + - + +
156A TRP 4.5 1.6 - - - +
157A GLY* 4.2 11.2 - - - +
233A ASN* 5.0 2.4 + - - -
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Residues in contact with HIS 148 (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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146A VAL* 3.5 6.1 - - - +
147A GLU* 1.3 83.9 - - + +
149A GLN* 1.3 76.1 + - - +
150A ASN* 3.4 21.4 + - - +
153A SER* 2.8 35.5 + - - -
154A VAL* 3.4 0.2 - - - -
155A GLN* 2.8 48.8 + - + +
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Residues in contact with GLN 149 (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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91A LEU* 4.2 9.7 + - + +
94A TYR* 3.4 42.0 + - + +
146A VAL* 3.8 14.1 - - + +
148A HIS* 1.3 84.5 + - - +
150A ASN* 1.3 93.4 + - - +
151A SER* 4.1 1.8 - - - +
153A SER 3.3 11.4 - - - +
154A VAL* 4.3 2.5 - - + -
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Residues in contact with ASN 150 (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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91A LEU* 3.7 4.0 - - - +
148A HIS* 3.4 19.2 + - - +
149A GLN* 1.3 92.9 + - - +
151A SER* 1.4 59.2 + - - +
152A LYS* 2.8 30.2 + - - +
153A SER* 2.8 40.1 + - - +
301A MES 3.6 30.3 - - - -
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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