Contacts of the strand formed by residues 91 - 98 (chain T) in PDB entry 5IY8
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 GLN 91 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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555B GLU* 3.1 30.1 + - - +
556B ILE* 3.5 15.3 - - - +
557B SER* 3.4 7.2 - - - +
30S ALA* 6.1 0.2 - - + -
31S PHE 3.4 10.5 - - - +
32S ASN* 4.5 1.3 - - - +
33S ALA* 3.8 7.0 - - - +
143S TRP* 5.2 1.7 - - - -
87T SER 4.7 2.8 + - - -
88T VAL* 2.9 32.4 - - - +
89T GLY 3.4 1.2 - - - -
90T GLY* 1.3 81.8 - - - +
92T THR* 1.3 63.2 + - - +
93T LEU* 3.6 28.2 + - + +
113T ARG* 3.5 30.1 - - - +
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Residues in contact with THR 92 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S MET 4.7 0.4 - - - -
30S ALA* 3.2 3.1 - - - -
31S PHE* 2.5 57.4 + - + +
32S ASN 4.0 0.3 + - - -
33S ALA* 3.7 18.7 + - - +
37S VAL* 3.9 14.5 - - + +
39S PHE* 3.9 30.5 - - + -
91T GLN* 1.3 75.8 + - - +
93T LEU* 1.3 69.2 + - - +
94T THR* 4.6 4.7 - - + -
109T ILE* 5.4 2.7 - - + -
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Residues in contact with LEU 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28S ILE* 4.6 4.3 - - + -
29S MET 3.8 2.7 - - - -
30S ALA* 3.5 20.9 - - + -
143S TRP* 3.8 21.5 - - + -
20T LEU* 4.2 7.2 - - + -
88T VAL* 4.9 4.7 - - + -
91T GLN* 3.6 29.6 + - + +
92T THR* 1.3 86.8 - - - +
94T THR* 1.3 62.8 - - - +
109T ILE* 3.3 8.5 - - - +
110T VAL* 2.9 49.6 + - + +
113T ARG* 3.5 37.9 - - + -
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Residues in contact with THR 94 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28S ILE* 3.5 8.3 - - - +
29S MET* 2.8 70.4 + - + +
31S PHE* 5.2 2.5 - - + -
39S PHE* 3.6 33.0 - - + -
92T THR* 4.6 3.1 - - + -
93T LEU* 1.3 81.2 - - - +
95T VAL* 1.3 65.3 + - - +
106T LEU* 4.4 9.6 - - + -
108T GLY 3.9 4.7 - - - -
109T ILE* 3.8 17.0 - - + -
110T VAL* 3.8 6.3 - - - +
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Residues in contact with VAL 95 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26S TYR* 5.0 7.4 - - + -
27S ASN 3.4 14.4 - - - +
28S ILE* 4.0 4.9 - - + -
126S ILE* 3.8 24.9 - - + -
138S PHE* 6.6 0.2 - - + -
18T VAL* 3.6 19.7 - - + -
94T THR* 1.3 72.9 - - - +
96T PHE* 1.3 68.1 + - - +
97T THR* 4.9 9.9 - - + -
106T LEU* 3.2 15.7 - - - +
107T GLU* 3.3 10.6 + - + -
108T GLY 2.6 29.8 + - - +
110T VAL* 3.5 26.2 - - + -
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Residues in contact with PHE 96 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27S ASN* 3.1 61.2 + - + +
28S ILE 3.3 25.8 - - - -
29S MET* 3.4 33.7 - - + -
47S LEU* 4.1 25.4 - - + -
98S TRP* 4.3 15.3 - + - -
144S TYR* 3.7 16.4 - + - -
146S PHE* 4.1 12.3 - + - -
7T LEU* 4.9 5.2 - - + -
95T VAL* 1.3 75.2 - - - +
97T THR* 1.3 69.1 + - - +
104T LEU* 4.7 3.8 - - + -
105T SER 3.4 11.2 - - - +
106T LEU* 3.9 12.6 - - + +
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Residues in contact with THR 97 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24S LYS* 5.0 8.4 + - - -
25S LYS 3.6 2.7 - - - -
26S TYR* 3.4 32.8 - - + -
95T VAL* 4.9 4.0 - - + -
96T PHE* 1.3 78.7 - - - +
98T GLU* 1.3 62.0 + - - +
99T SER* 4.1 2.6 + - - -
103T LYS 4.6 0.4 - - - -
104T LEU* 3.4 13.4 - - - +
105T SER* 2.6 56.8 + - - -
107T GLU* 3.1 39.6 + - + +
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Residues in contact with GLU 98 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23S THR 4.9 0.2 - - - +
24S LYS* 3.4 1.7 - - - -
25S LYS* 2.8 56.5 + - + +
27S ASN* 3.1 27.0 + - - +
49S ARG* 3.9 16.5 + - - -
98S TRP* 3.9 20.6 - - - -
141S HIS* 5.2 2.9 - - - -
144S TYR* 5.2 1.6 + - - -
97T THR* 1.3 75.0 - - - +
99T SER* 1.3 67.9 + - - +
104T LEU* 4.0 14.8 - - + -
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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