Contacts of the strand formed by residues 153 - 160 (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 SER 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A LEU* 3.1 16.8 - - - -
83A LYS* 3.9 17.1 - - - +
91A LEU* 3.7 8.1 - - - +
148A HIS* 2.8 32.1 - - - -
149A GLN* 3.3 3.4 - - - -
150A ASN* 2.8 41.1 + - - +
151A SER 3.8 0.2 - - - -
152A LYS* 1.3 80.4 - - - +
154A VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 154 (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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80A ILE 4.2 0.2 - - - +
81A GLY* 3.4 1.7 - - - -
82A LEU* 2.9 43.7 + - + +
91A LEU* 3.6 19.7 - - + -
94A TYR* 3.9 36.6 - - + -
146A VAL* 4.3 7.2 - - + -
148A HIS* 3.4 10.8 - - - +
149A GLN* 4.3 2.0 - - + -
153A SER* 1.3 76.0 - - - +
155A GLN* 1.3 65.1 + - - +
156A TRP* 3.8 34.2 - - + -
212A ALA* 4.4 6.5 - - + -
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Residues in contact with GLN 155 (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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79A ASN* 3.7 25.8 - - - +
80A ILE 3.3 11.4 - - - +
81A GLY* 3.4 16.0 - - - -
146A VAL* 3.5 3.3 - - - +
147A GLU* 2.7 58.0 + - + +
148A HIS* 2.8 29.9 + - + +
154A VAL* 1.3 76.2 - - - +
156A TRP* 1.3 57.9 + - - +
229A THR* 3.7 12.6 - - - +
262A ASN* 5.0 5.9 + - - -
264A ASN* 5.0 2.6 - - - +
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Residues in contact with TRP 156 (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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50A MET* 4.2 11.4 - - + -
78A TYR 3.7 0.5 - - - +
79A ASN* 3.7 5.5 - - - -
80A ILE* 2.8 58.8 + - + +
81A GLY* 5.3 0.4 - - - -
82A LEU 5.5 0.2 - - - -
94A TYR* 3.8 17.0 - + + -
95A LEU 3.4 20.2 - - - -
96A PRO* 2.7 33.3 + - + +
144A SER* 5.5 0.9 - - - -
145A GLU* 3.5 10.3 - - - +
146A VAL* 3.7 20.4 - - + +
147A GLU* 4.4 2.7 - - - +
154A VAL* 3.8 33.9 - - + -
155A GLN* 1.3 81.8 - - - +
157A GLY* 1.3 58.8 + - - +
158A ILE* 4.1 8.9 - - + +
210A PHE* 3.5 46.0 - + + -
211A ILE 3.8 14.1 - - - -
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Residues in contact with GLY 157 (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* 3.7 24.0 - - - -
78A TYR 3.5 5.8 - - - -
143A ILE 3.5 3.5 - - - +
144A SER* 3.5 0.9 - - - -
145A GLU* 2.9 34.7 + - - +
147A GLU* 4.2 7.9 - - - +
156A TRP* 1.3 73.2 - - - +
158A ILE* 1.4 61.1 + - - +
159A LYS* 3.8 3.6 - - - +
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Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLN* 3.3 2.3 - - - +
78A TYR* 2.8 49.7 + - + +
80A ILE* 3.8 13.2 - - + -
139A GLN* 3.8 21.8 - - + +
142A TYR* 3.3 13.1 - - + -
143A ILE 3.3 3.4 - - - -
144A SER* 3.5 16.6 - - - +
156A TRP* 4.1 9.9 - - + +
157A GLY* 1.4 74.6 - - - +
159A LYS* 1.3 58.9 + - - +
201A LEU* 4.0 25.1 - - + -
206A PHE* 3.7 28.7 - - + -
210A PHE* 3.6 23.1 - - + -
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Residues in contact with LYS 159 (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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76A PHE* 3.2 36.1 - - + +
77A GLN* 3.7 22.9 - - + +
142A TYR* 3.1 7.8 - - - -
143A ILE* 2.9 53.6 + - + +
145A GLU* 5.9 3.1 + - - -
157A GLY 5.2 2.0 - - - +
158A ILE* 1.3 73.7 - - - +
160A ALA* 1.4 69.7 + - - +
161A ASN* 5.8 0.9 - - - +
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Residues in contact with ALA 160 (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 TRP* 3.8 30.3 - - + -
76A PHE* 2.8 31.2 + - + +
141A ASN 4.0 2.7 - - - -
142A TYR* 3.4 12.8 - - + -
159A LYS* 1.4 78.4 - - - +
161A ASN* 1.3 58.5 + - - +
163A PHE* 3.9 16.4 - - + -
172A GLY* 3.7 15.7 - - - -
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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