Contacts of the strand formed by residues 100 - 106 (chain A) in PDB entry 1EFU
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 GLY 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASN 3.4 2.5 + - - +
14A VAL* 3.3 26.5 - - - +
15A GLY 3.4 2.3 + - - -
98A MET* 3.4 5.0 - - - +
99A ASP* 1.3 82.2 - - - +
101A ALA* 1.3 59.7 + - - +
127A VAL* 4.1 4.9 - - - -
129A TYR 3.3 12.6 - - - -
199A ILE* 3.5 24.1 - - - +
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Residues in contact with ALA 101 (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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15A GLY 3.5 9.0 - - - +
17A ILE* 4.7 14.6 - - + -
98A MET* 4.0 14.6 - - + -
100A GLY* 1.3 75.0 - - - +
102A ILE* 1.3 64.8 + - - +
103A LEU 3.8 0.6 + - - -
122A GLY* 6.2 0.4 - - - -
127A VAL* 3.8 18.4 - - + +
129A TYR 2.9 8.3 + - - +
130A ILE* 3.2 15.0 - - + -
131A ILE* 2.8 27.3 + - - +
199A ILE* 4.8 0.6 - - - +
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Residues in contact with ILE 102 (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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14A VAL* 5.0 5.8 - - + -
15A GLY 2.9 12.7 + - - +
16A THR* 3.5 7.4 - - + -
17A ILE* 3.2 24.0 + - - -
27A LEU* 4.1 21.3 - - + -
31A ILE* 4.4 10.8 - - + -
69A TYR* 4.5 6.3 - - - +
78A HIS* 4.6 9.6 - - + -
100A GLY 5.5 0.2 - - - +
101A ALA* 1.3 74.8 - - - +
103A LEU* 1.3 67.3 + - - +
104A VAL* 3.6 3.7 + - + +
131A ILE* 3.1 11.9 - - + +
133A PHE* 4.1 10.8 - - + -
191A LEU* 4.3 21.5 - - + -
195A LEU* 3.8 40.2 - - + -
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Residues in contact with LEU 103 (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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17A ILE* 3.3 29.6 - - + +
18A GLY* 4.6 1.6 - - - -
101A ALA 3.8 2.2 + - - -
102A ILE* 1.3 72.8 - - - +
104A VAL* 1.3 61.1 + - - +
105A VAL* 3.9 20.9 - - + -
115A THR* 4.1 17.9 - - + -
118A HIS* 4.1 24.2 - - + +
119A ILE* 4.2 18.2 - - + +
130A ILE* 3.9 19.7 - - + +
131A ILE 2.8 8.1 + - - +
132A VAL* 3.4 10.5 - - + +
133A PHE 3.0 25.3 + - - -
153A VAL* 4.2 19.3 - - + -
157A LEU* 4.9 1.3 - - + -
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Residues in contact with VAL 104 (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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16A THR* 4.1 12.3 - - + -
17A ILE 3.2 6.4 + - - +
18A GLY* 3.8 16.1 - - - -
19A HIS 4.3 0.3 + - - -
22A HIS* 3.6 33.4 + - - +
23A GLY 4.3 12.6 - - - +
24A LYS* 4.3 16.8 - - + -
27A LEU* 3.6 29.8 - - + -
102A ILE* 3.9 11.9 - - + +
103A LEU* 1.3 75.5 - - - +
105A VAL* 1.3 66.9 + - - +
133A PHE* 3.6 11.0 - - + +
135A ASN* 4.2 10.3 - - + +
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Residues in contact with VAL 105 (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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22A HIS* 3.6 6.5 - - + +
103A LEU* 3.9 29.1 + - + -
104A VAL* 1.3 79.2 - - - +
106A ALA* 1.3 62.9 + - - +
107A ALA 3.5 0.2 + - - -
110A GLY* 3.3 40.8 - - - +
111A PRO* 3.6 8.5 - - + -
115A THR* 4.7 11.4 - - + +
132A VAL* 4.7 4.7 - - + +
133A PHE 3.3 5.3 + - - -
134A LEU* 3.1 22.8 - - + +
135A ASN* 2.7 24.6 + - - -
153A VAL* 4.6 9.9 - - + -
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Residues in contact with ALA 106 (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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22A HIS* 3.1 36.6 + - + +
105A VAL* 1.3 73.3 - - - +
107A ALA* 1.3 60.9 + - - +
108A THR* 3.0 18.5 + - - +
109A ASP* 3.1 2.3 + - - +
110A GLY* 2.9 26.2 + - - +
135A ASN* 3.4 10.5 - - + +
136A LYS* 3.7 21.3 - - + +
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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