Contacts of the strand formed by residues 106 - 115 (chain B) in PDB entry 1E50
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 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B VAL* 4.5 2.0 - - + -
8B GLN* 3.6 17.3 - - + +
11B LYS* 3.7 21.3 - - + -
12B PHE* 4.1 13.2 - - + -
18B PHE* 3.4 31.2 - - + -
102B ILE* 3.8 3.1 - - - +
103B LEU 2.9 23.6 + - - -
104B ASN 3.4 13.5 - - - +
105B GLY* 1.3 82.4 - - - +
107B CYS* 1.3 63.2 + - - +
108B VAL* 3.2 26.0 + - + +
127B PHE* 4.7 1.3 - - + -
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Residues in contact with CYS 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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4B VAL* 4.1 1.3 - - - -
8B GLN* 2.7 24.0 + - - +
101B MET 3.7 7.2 - - - +
102B ILE* 4.0 8.5 - - - +
105B GLY 4.3 0.2 - - - -
106B VAL* 1.3 68.4 - - - +
108B VAL* 1.3 64.3 + - - +
127B PHE* 3.6 9.2 - - - -
128B ASP* 3.0 19.4 + - + +
131B ARG* 3.5 42.0 - - + +
132B ALA* 3.8 21.8 - - - +
135B GLU* 3.6 17.5 - - - -
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Residues in contact with VAL 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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12B PHE* 4.0 17.7 - - + -
18B PHE* 4.1 7.0 - - + -
100B PRO* 3.6 1.7 - - - +
101B MET* 3.0 53.9 + - + +
103B LEU* 4.0 12.1 - - + -
106B VAL* 3.2 32.8 - - + +
107B CYS* 1.3 75.2 - - - +
109B ILE* 1.3 70.0 + - - +
125B LEU* 4.1 22.4 - - + -
126B GLU 3.0 14.1 - - - +
127B PHE* 4.7 0.2 - - - -
128B ASP* 4.0 2.8 - - - +
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Residues in contact with ILE 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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98B LYS* 3.7 45.3 - - + +
99B ALA 3.6 8.3 - - - +
100B PRO* 4.7 5.8 - - + -
108B VAL* 1.3 77.3 - - - +
110B TRP* 1.3 62.1 + - - +
111B LYS* 3.7 21.8 + - + +
124B CYS 3.7 0.5 - - - +
125B LEU* 3.5 4.3 - - - -
126B GLU* 2.7 49.1 + - + +
127B PHE 5.4 0.2 - - - +
128B ASP* 2.9 42.6 - - + +
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Residues in contact with TRP 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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27B ILE* 3.7 24.7 - - + +
55B ILE* 3.4 47.7 + - + +
57B PHE* 3.5 22.9 - + - -
64B LEU* 3.6 18.8 - - + +
66B LEU* 3.4 32.1 - - + +
97B LEU* 3.7 30.7 - - + -
98B LYS* 3.4 2.9 - - - -
99B ALA* 2.8 47.3 + - + +
101B MET* 4.9 3.6 - - - -
108B VAL* 5.0 0.6 - - - +
109B ILE* 1.3 71.0 - - - +
111B LYS* 1.3 65.1 + - - +
112B GLY* 3.7 15.5 - - - -
123B GLY* 4.9 0.2 - - - -
124B CYS 3.4 7.2 - - - -
125B LEU* 3.5 25.5 - - + +
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Residues in contact with LYS 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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97B LEU 3.3 5.6 - - - +
98B LYS* 4.5 21.3 - - + +
109B ILE* 3.8 26.0 - - + +
110B TRP* 1.3 82.2 - - - +
112B GLY* 1.3 58.9 + - - +
123B GLY* 3.0 1.2 - - - -
124B CYS* 2.7 44.0 + - - +
126B GLU* 2.8 45.4 + - + +
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Residues in contact with GLY 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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96B TYR* 3.5 6.4 - - - +
97B LEU* 2.7 37.5 + - - +
110B TRP* 3.7 13.2 - - - -
111B LYS* 1.3 76.6 - - - +
113B TRP* 1.3 60.8 + - - -
122B MET 3.1 14.6 - - - -
123B GLY* 3.5 4.0 - - - -
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Residues in contact with TRP 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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24B GLU* 4.1 9.6 + - - -
27B ILE* 3.4 1.2 - - - +
94B LYS* 3.3 42.8 - - + +
95B VAL 3.0 13.5 - - - +
96B TYR* 3.8 44.5 + + + -
97B LEU* 5.4 1.1 - - - -
112B GLY* 1.3 75.1 - - - +
114B ILE* 1.3 74.7 + - - +
115B ASP* 4.2 13.2 - - + -
120B ASP 4.2 0.9 - - - -
121B GLY* 3.3 19.2 - - - -
122B MET* 2.8 68.4 + - + +
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Residues in contact with ILE 114 (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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27B ILE* 4.0 10.1 - - + -
28B LYS* 4.6 0.7 - - - -
29B TYR* 3.9 17.7 - - + +
44B PHE* 3.4 37.7 - - + -
55B ILE* 3.4 41.5 - - + -
94B LYS* 3.1 5.1 - - - +
95B VAL* 3.0 33.6 + - + +
97B LEU* 5.0 1.5 - - + +
113B TRP* 1.3 81.6 - - - +
115B ASP* 1.3 75.3 + - - +
116B LEU* 3.3 1.2 + - - +
119B LEU* 3.8 12.3 - - - +
120B ASP 3.4 12.8 - - - +
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Residues in contact with ASP 115 (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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93B GLY* 4.4 7.8 - - - +
94B LYS* 3.8 12.8 - - - +
113B TRP* 4.0 10.6 - - + -
114B ILE* 1.3 71.5 - - - +
116B LEU* 1.3 60.5 + - - +
117B GLN* 2.8 23.3 + - - +
118B ARG* 2.7 49.2 + - + +
119B LEU* 2.6 32.6 + - - -
120B ASP 2.8 16.7 + - - +
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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