Contacts of the strand formed by residues 102 - 113 (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 ILE 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B THR* 4.7 6.1 - - - +
7B THR 5.1 0.7 - - - +
8B SER* 3.6 25.4 - - - -
97B ILE 3.4 1.7 - - - +
98B THR* 3.3 5.0 - - - +
99B VAL* 2.9 35.6 + - - +
100B GLY 3.4 1.8 + - - -
101B GLY* 1.3 82.9 - - - +
103B THR* 1.3 68.8 + - - +
104B VAL* 4.8 0.4 - - + -
147B ILE* 4.0 30.5 - - + -
150B GLN* 3.8 19.7 - - - +
152B VAL* 4.6 15.9 - - + -
153B LEU* 3.7 25.6 - - + -
178B LEU* 5.3 3.4 - - + -
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Residues in contact with THR 103 (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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96B ILE* 3.7 20.2 - - + -
97B ILE 3.4 3.8 - - - -
98B THR* 3.9 22.4 - - + +
101B GLY 4.4 1.1 + - - +
102B ILE* 1.3 75.5 - - - +
104B VAL* 1.3 54.2 + - - +
150B GLN* 2.8 27.1 + - - +
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Residues in contact with VAL 104 (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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96B ILE* 4.3 3.1 - - - -
97B ILE* 2.8 44.0 + - + +
99B VAL* 5.1 1.6 - - + -
102B ILE* 5.1 0.7 - - + -
103B THR* 1.3 74.9 - - - +
105B THR* 1.3 69.9 + - - +
106B GLN* 3.3 4.6 + - + +
143B ILE* 3.7 32.8 - - + -
146B ASN* 3.6 38.1 - - + +
147B ILE* 3.9 14.8 - - + +
150B GLN* 3.5 18.8 - - - +
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Residues in contact with THR 105 (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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94B GLN* 3.5 34.1 - - + +
95B ASP* 3.6 9.9 - - - +
96B ILE* 4.0 15.2 - - + +
104B VAL* 1.3 81.0 - - - +
106B GLN* 1.3 59.6 + - - +
146B ASN* 3.7 12.5 + - - -
150B GLN* 4.8 1.0 - - - +
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Residues in contact with GLN 106 (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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44B VAL* 4.1 16.2 - - + +
94B GLN* 3.4 7.7 - - - +
95B ASP 2.9 30.8 + - - +
97B ILE* 3.8 31.6 - - + -
104B VAL* 3.9 10.7 - - + +
105B THR* 1.3 74.8 - - - +
107B MET* 1.3 84.3 + - - +
108B PHE* 3.8 3.3 - - - -
140B VAL* 4.5 0.8 - - - +
141B THR 2.9 22.4 + - - -
142B PRO* 4.0 1.2 - - - +
143B ILE* 3.2 32.0 - - + +
146B ASN* 2.7 27.0 + - - +
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Residues in contact with MET 107 (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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44B VAL* 4.5 3.6 + - - +
75B ASN* 5.0 5.8 - - + -
92B LEU* 3.7 31.4 - - + -
93B SER 3.3 9.2 - - - +
94B GLN* 3.6 29.8 - - - +
106B GLN* 1.3 99.9 + - - +
108B PHE* 1.3 59.4 + - - +
140B VAL* 3.5 32.7 - - + +
141B THR* 5.3 2.0 - - - +
146B ASN* 4.8 2.6 - - - +
401B NAG 3.8 33.4 - - - +
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Residues in contact with PHE 108 (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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26B ILE* 3.7 14.4 - - + -
44B VAL* 3.3 29.4 - - + +
46B VAL* 3.9 21.3 - - + -
64B PHE* 3.6 27.1 - + - -
72B TYR* 5.4 0.2 - + - -
92B LEU* 3.5 9.7 - - - +
93B SER* 2.7 60.0 + - - +
95B ASP* 3.7 29.2 - - + -
97B ILE* 4.3 13.9 - - + -
106B GLN 3.8 9.9 - - - -
107B MET* 1.3 75.1 - - - +
109B GLY* 1.3 69.0 + - - +
110B GLU* 3.7 21.5 - - + -
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Residues in contact with GLY 109 (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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44B VAL 2.7 16.2 + - - -
45B TRP* 3.2 9.5 - - - +
46B VAL 3.0 28.1 + - - +
79B LEU* 4.2 21.8 - - - +
81B LEU* 5.4 0.2 - - - -
91B PHE 3.4 6.5 - - - -
92B LEU* 4.5 0.8 - - - +
108B PHE* 1.3 78.2 - - - +
110B GLU* 1.3 61.9 + - - -
111B VAL* 3.9 1.1 - - - -
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Residues in contact with GLU 110 (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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46B VAL 3.5 3.8 - - - +
48B SER* 2.8 31.0 + - - -
49B SER* 4.9 1.0 + - - -
64B PHE* 3.5 32.8 - - + +
66B ALA* 4.0 8.1 + - - +
72B TYR* 3.8 7.6 + - - -
90B GLY* 3.1 2.9 - - - -
91B PHE* 2.6 66.8 + - + +
93B SER* 2.6 27.2 + - - +
108B PHE* 3.7 18.5 + - + -
109B GLY* 1.3 70.7 - - - -
111B VAL* 1.3 61.2 - - - +
112B THR 3.9 0.3 + - - -
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Residues in contact with VAL 111 (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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45B TRP* 3.4 40.8 - - + -
46B VAL 2.8 16.7 + - - +
47B PRO* 3.6 4.8 - - + +
48B SER* 2.8 27.9 + - - +
51B CYS* 3.8 6.8 - - - +
79B LEU* 6.3 0.2 - - + -
81B LEU* 4.9 3.1 - - + -
88B VAL* 3.6 27.1 - - + -
89B SER 3.5 13.9 - - - +
90B GLY* 5.0 0.4 - - - -
109B GLY* 4.3 1.6 - - - +
110B GLU* 1.3 74.4 - - - +
112B THR* 1.3 63.5 + - - +
113B GLU 3.8 19.7 - - - +
114B MET* 4.4 10.8 - - + -
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Residues in contact with THR 112 (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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48B SER* 4.2 1.3 - - - -
50B LYS* 3.4 31.0 - - + +
51B CYS* 3.4 25.2 - - - +
52B SER* 4.0 4.7 + - - -
55B TYR* 3.7 11.8 - - - -
89B SER* 3.2 8.5 + - - -
90B GLY* 3.8 9.0 - - - -
91B PHE* 4.1 25.7 - - + -
111B VAL* 1.3 77.1 - - - +
113B GLU* 1.3 63.9 + - - +
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Residues in contact with GLU 113 (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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55B TYR* 3.4 24.9 + - + +
88B VAL* 3.3 22.9 - - - +
89B SER* 3.2 41.8 + - - +
111B VAL* 4.1 0.9 - - - -
112B THR* 1.3 81.1 + - - +
114B MET* 1.3 59.4 + - - +
115B PRO* 3.6 7.3 - - + +
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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