Contacts of the strand formed by residues 88 - 99 (chain B) in PDB entry 5T4S
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 VAL 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TRP* 4.4 14.8 - - + +
79B LEU 4.2 0.2 - - - +
80B THR* 3.4 4.7 - - - +
81B LEU* 2.7 60.1 + - + +
87B THR* 1.3 79.3 - - - +
89B SER* 1.3 63.7 + - - +
111B VAL* 3.6 33.9 - - + -
113B GLU 3.3 20.2 - - - +
114B MET* 4.5 1.8 - - + -
119B PHE* 3.5 31.6 - - + -
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 6.3 2.0 - - - -
79B LEU 3.5 9.4 - - - -
80B THR* 3.4 19.9 + - - +
81B LEU* 5.7 0.2 - - - -
87B THR* 5.5 1.6 - - - +
88B VAL* 1.3 78.3 - - - +
90B GLY* 1.3 58.6 + - - +
111B VAL* 3.5 6.5 - - - +
112B THR* 3.2 6.0 + - - -
113B GLU* 3.2 57.3 + - - +
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 3.6 13.7 - - - +
79B LEU* 3.0 36.2 + - - +
81B LEU* 5.5 0.6 - - - +
89B SER* 1.3 75.7 - - - +
91B PHE* 1.3 62.4 + - - -
110B GLU 3.1 13.9 - - - -
111B VAL* 4.2 1.9 - - - +
112B THR* 3.8 13.0 - - - -
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER* 4.0 10.8 - - - -
50B LYS* 4.3 11.4 - - + -
72B TYR* 4.4 9.2 - - - -
74B HIS* 5.5 4.0 - + - -
76B GLY* 3.7 28.5 - - - +
77B THR 3.3 5.2 - - - +
78B GLU* 4.9 5.6 - - - +
79B LEU* 3.6 4.9 - - - -
90B GLY* 1.3 74.2 - - - +
92B LEU* 1.3 65.0 + - - +
93B SER* 3.4 9.6 - - - -
109B GLY* 3.4 1.6 - - - -
110B GLU* 2.6 86.8 + - + +
112B THR* 4.1 18.4 - - + -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ASN* 5.6 0.2 - - - +
75B ASN* 3.3 28.3 + - - +
76B GLY* 2.8 27.9 + - - -
77B THR* 2.8 26.7 + - + +
79B LEU* 4.0 24.7 - - + +
91B PHE* 1.3 74.6 - - - +
93B SER* 1.3 64.8 + - - +
107B MET* 3.7 31.9 - - + -
108B PHE* 3.5 17.9 - - - +
138B GLY 5.8 2.0 - - - +
140B VAL* 4.2 20.6 - - + -
401B NAG 4.5 10.1 - - - +
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.5 15.0 + - - -
73B LYS 4.3 4.3 - - - -
75B ASN* 4.6 3.4 - - - +
91B PHE* 3.4 8.0 - - - -
92B LEU* 1.3 75.1 + - - +
94B GLN* 1.3 60.5 + - - +
107B MET* 3.3 7.4 - - - +
108B PHE* 2.7 58.8 + - - -
110B GLU* 2.6 34.6 + - - +
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Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B SER 3.9 1.1 - - - +
72B TYR* 3.4 4.0 - - - -
73B LYS* 2.8 62.8 + - + +
75B ASN* 5.3 2.0 - - + +
93B SER* 1.3 75.9 - - - +
95B ASP* 1.3 66.3 + - - +
105B THR* 3.5 29.1 - - + +
106B GLN 3.4 14.1 - - - +
107B MET* 3.6 27.4 - - - +
108B PHE* 4.0 1.6 - - - -
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Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 3.8 8.3 - - + -
27B GLY* 3.3 11.8 - - - -
64B PHE* 3.5 8.6 - - + -
69B SER* 2.6 27.5 + - - -
71B SER* 2.6 34.6 + - - -
72B TYR* 3.4 16.5 - - - +
94B GLN* 1.3 74.5 - - - +
96B ILE* 1.3 74.0 + - - +
97B ILE* 3.6 2.9 + - - +
104B VAL 3.6 0.3 - - - +
105B THR* 3.6 3.8 - - - -
106B GLN* 2.9 33.6 + - - +
108B PHE* 3.7 18.2 - - + -
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLY 3.7 0.7 - - - +
26B ILE* 3.5 1.9 - - - -
27B GLY* 2.9 34.7 + - - +
28B THR* 4.2 9.6 - - - +
71B SER* 3.7 26.9 - - - +
95B ASP* 1.3 82.8 + - - +
97B ILE* 1.3 63.4 + - - +
98B THR* 4.2 3.1 + - - +
103B THR* 3.7 33.7 - - + -
104B VAL 3.5 8.5 - - - +
105B THR* 4.0 16.6 - - + +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 4.0 16.8 - - + -
25B GLY 3.1 8.7 - - - +
26B ILE* 3.8 27.4 - - + -
44B VAL* 4.0 21.5 - - + -
95B ASP 4.3 2.7 - - - +
96B ILE* 1.3 75.6 - - - +
98B THR* 1.3 63.5 + - - +
99B VAL* 3.8 21.2 + - + -
102B ILE 3.4 4.3 - - - +
103B THR* 3.4 1.6 - - - -
104B VAL* 2.8 39.6 + - + +
106B GLN* 3.8 31.4 - - + -
108B PHE* 4.3 9.2 - - + -
143B ILE* 3.8 11.9 - - + -
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU 4.3 0.5 - - - +
24B ILE* 3.2 10.7 - - - +
25B GLY* 2.8 44.1 + - - -
27B GLY 5.6 0.5 + - - -
30B PRO* 4.5 16.5 - - + +
96B ILE* 4.2 3.5 + - - +
97B ILE* 1.3 70.7 - - - +
99B VAL* 1.3 62.0 + - - +
100B GLY 3.7 19.8 + - - +
101B GLY 5.4 0.7 - - - -
102B ILE 3.3 9.9 - - - +
103B THR* 3.9 18.2 - - + +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B SER* 3.1 11.9 + - - -
10B VAL* 3.7 21.5 - - + -
23B GLU 4.9 0.9 - - - -
24B ILE* 3.9 9.4 - - + -
37B PHE* 4.0 20.6 - - + -
97B ILE* 3.8 22.9 - - + +
98B THR* 1.3 76.2 - - - +
100B GLY* 1.3 63.1 + - - +
102B ILE* 2.9 23.4 + - + +
104B VAL* 5.1 0.4 - - + -
128B VAL* 6.0 0.2 - - + -
143B ILE* 3.8 17.7 - - + -
147B ILE* 4.7 9.6 - - + -
178B LEU* 3.9 22.1 - - + +
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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