Contacts of the strand formed by residues 102 - 107 (chain A) in PDB entry 1EFT
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 ALA 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A GLY 3.7 4.9 - - - +
17A ILE* 3.9 28.9 - - + -
99A MET* 4.0 13.7 - - - -
101A GLY* 1.3 74.4 - - - -
103A ILE* 1.3 65.3 + - - +
104A LEU 3.8 0.9 - - - +
128A VAL* 3.8 16.6 - - + +
130A TYR 3.0 9.0 + - - +
131A ILE* 3.7 8.2 - - + -
132A VAL* 3.1 24.0 + - - +
210A ILE* 4.2 3.9 - - - +
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Residues in contact with ILE 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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14A VAL* 4.3 7.6 - - + -
15A GLY 2.8 15.3 + - - +
16A THR* 3.4 6.3 - - + -
17A ILE* 3.1 22.4 + - - -
27A LEU* 4.0 23.6 - - + -
31A LEU* 4.6 7.4 - - + -
70A TYR* 4.2 11.0 - - - +
79A HIS* 4.0 26.9 - - + +
102A ALA* 1.3 74.1 - - - +
104A LEU* 1.3 60.8 + - - +
105A VAL* 3.5 3.6 + - + +
132A VAL* 3.4 8.5 - - + +
134A PHE* 4.2 17.0 - - + -
202A LEU* 4.4 14.4 - - + -
206A ILE* 3.8 31.9 - - + -
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Residues in contact with LEU 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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17A ILE* 3.6 26.9 - - + +
18A GLY* 4.4 7.9 - - - -
102A ALA 3.8 2.0 - - - -
103A ILE* 1.3 72.3 - - - +
105A VAL* 1.3 61.9 + - - +
106A VAL* 3.9 8.3 - - + -
116A THR* 3.7 29.8 - - + +
119A HIS* 5.3 0.7 - - + -
120A ILE* 4.1 22.9 - - + -
131A ILE* 4.1 9.6 - - + +
132A VAL 2.9 14.4 + - - +
133A VAL* 3.4 15.4 - - + +
134A PHE 2.9 24.4 + - - +
154A VAL* 3.9 28.5 - - + -
158A LEU* 4.5 7.4 - - + -
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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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16A THR* 4.3 2.5 - - + -
17A ILE 2.9 11.6 + - - +
18A GLY* 3.6 17.8 - - - -
19A HIS 4.3 0.5 + - - -
22A HIS* 3.6 33.7 + - + +
23A GLY 3.8 15.0 - - - +
24A LYS* 3.9 19.7 - - + +
27A LEU* 3.5 30.3 - - + -
103A ILE* 4.1 11.7 - - + +
104A LEU* 1.3 75.5 - - - +
106A VAL* 1.3 63.9 + - - +
116A THR* 5.3 1.0 + - - -
134A PHE* 3.5 8.1 - - + +
136A ASN* 4.1 13.0 - - + -
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Residues in contact with VAL 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* 3.8 8.1 - - + +
104A LEU* 3.9 20.9 - - + -
105A VAL* 1.3 79.9 - - - +
107A SER* 1.3 64.4 + - - +
108A ALA 3.5 0.2 + - - -
111A GLY* 3.6 33.0 - - - +
112A PRO* 3.7 13.7 - - + -
116A THR* 4.2 8.3 - - + +
133A VAL* 4.2 8.3 - - + -
134A PHE 3.1 5.6 + - - +
135A MET* 3.4 10.9 - - + +
136A ASN 2.8 22.5 + - - -
150A VAL* 4.6 1.8 - - + -
154A VAL* 4.1 26.5 - - + -
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Residues in contact with SER 107 (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* 3.2 33.5 + - - -
106A VAL* 1.3 72.5 - - - +
108A ALA* 1.3 55.3 + - - +
109A ALA* 3.4 3.8 + - - +
110A ASP* 2.6 30.6 + - - -
111A GLY* 2.6 36.0 + - - -
136A ASN 3.6 5.8 - - - -
137A LYS* 3.7 23.8 - - - +
150A VAL* 4.8 0.2 - - - +
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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