Contacts of the strand formed by residues 26 - 32 (chain A) in PDB entry 1WE7
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 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ASN* 5.0 9.9 - - + +
24A GLY* 4.4 6.1 - - - -
25A PRO* 1.3 77.7 - - - +
27A SER* 1.3 62.0 + - - +
28A ILE* 3.9 18.5 + - + -
50A PHE 3.7 2.9 - - - +
51A THR* 3.4 4.0 - - - -
52A LEU 3.3 32.6 + - - +
54A LEU* 3.6 33.6 - - + +
91A LEU* 5.8 2.9 - - + -
96A MET* 5.4 8.7 - - + +
97A ALA 4.5 3.6 - - - +
98A SER* 3.7 34.1 - - - +
99A GLY 4.8 0.2 - - - +
100A ALA* 6.1 0.4 - - + -
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Residues in contact with SER 27 (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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26A VAL* 1.3 71.8 - - - +
28A ILE* 1.3 62.1 + - - +
49A VAL* 4.6 11.3 - - - +
50A PHE 4.3 4.0 - - - -
51A THR* 3.1 26.8 + - - +
98A SER* 4.4 1.2 - - - +
99A GLY* 2.9 41.5 - - - +
100A ALA 2.9 3.4 + - - +
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Residues in contact with ILE 28 (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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26A VAL* 4.2 20.9 - - + +
27A SER* 1.3 76.8 - - - +
29A LYS* 1.3 62.1 + - - +
30A VAL* 3.3 33.0 - - + -
48A LEU 4.3 1.1 - - - +
49A VAL* 3.3 23.9 - - - +
50A PHE* 3.4 22.3 + - + +
61A ILE* 4.5 16.8 - - + -
91A LEU* 5.6 7.0 - - + -
96A MET* 5.2 9.2 - - - -
100A ALA* 3.3 26.0 - - + +
102A ILE* 4.2 16.4 - - + -
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Residues in contact with LYS 29 (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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28A ILE* 1.3 75.3 - - - +
30A VAL* 1.3 64.4 + - - +
31A GLN* 5.6 3.4 - - + +
47A GLY* 5.0 10.5 - - - -
48A LEU 3.8 1.6 - - - +
49A VAL* 3.5 22.9 - - + -
100A ALA 2.9 16.2 + - - +
101A VAL* 3.3 20.2 - - + +
102A ILE 2.6 32.4 + - - +
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Residues in contact with VAL 30 (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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28A ILE* 3.3 25.8 - - + -
29A LYS* 1.3 71.7 - - - +
31A GLN* 1.3 64.1 + - - +
32A VAL* 3.1 20.6 + - + +
47A GLY* 3.3 3.9 - - - -
48A LEU* 2.8 47.0 + - + +
50A PHE* 5.0 3.1 - - + -
61A ILE* 4.5 4.7 - - + -
65A ILE* 3.8 37.9 - - + -
78A LEU* 5.0 2.9 - - + -
102A ILE* 3.2 14.4 - - + +
104A LEU* 4.6 12.1 - - + -
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Residues in contact with GLN 31 (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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29A LYS* 3.7 6.4 + - + +
30A VAL* 1.3 68.2 - - - +
32A VAL* 1.3 77.7 + - - +
33A PRO* 3.3 9.2 - - - +
45A GLY* 5.2 1.2 - - - -
46A GLN 3.4 16.7 + - - +
47A GLY* 4.9 1.1 - - - -
101A VAL* 5.2 6.1 - - + -
102A ILE 3.0 15.2 + - - +
103A HIS* 4.2 25.8 - - + +
104A LEU* 3.0 28.9 + - - +
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Residues in contact with VAL 32 (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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30A VAL* 3.4 20.2 - - + +
31A GLN* 1.3 78.9 + - - +
33A PRO* 1.3 66.7 - - + +
42A LYS 4.0 9.9 - - - +
43A LEU* 3.2 31.6 - - + -
45A GLY* 3.3 3.1 - - - -
46A GLN* 2.8 60.0 + - + +
48A LEU* 3.7 30.7 - - + -
65A ILE* 5.9 1.1 - - + -
69A THR* 5.1 2.9 - - + -
104A LEU* 4.4 3.8 - - + -
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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