Contacts of the strand formed by residues 4 - 8 (chain E) in PDB entry 3HYW
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 HIS 4 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ALA 5.1 1.8 - - - +
3E LYS* 1.3 74.6 - - - +
5E VAL* 1.3 79.9 + - - +
6E VAL* 5.2 1.3 - - + -
29E LYS* 3.4 40.7 + - + +
31E THR* 2.7 30.9 + - - -
72E GLU* 5.0 0.4 - - - -
96E ILE* 3.8 15.9 - - + -
97E GLU 2.9 27.5 + - - +
98E TYR* 3.9 1.9 - - - -
99E ASP* 2.7 45.5 + - - +
100E TYR 3.1 6.9 + - - +
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Residues in contact with VAL 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E HIS* 1.3 77.8 - - - +
6E VAL* 1.3 71.0 + - - +
7E VAL* 4.3 4.5 - - + -
21E LEU* 3.7 23.1 - - + -
28E LEU* 3.7 26.2 - - + -
29E LYS 2.9 9.6 + - - +
30E ILE* 3.4 7.5 - - + +
31E THR 3.0 25.1 + - - +
100E TYR* 3.3 33.4 - - + +
102E VAL* 4.3 12.6 - - + -
328E ILE* 4.0 15.9 - - + -
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Residues in contact with VAL 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E HIS* 4.2 2.0 - - - +
5E VAL* 1.3 75.7 - - - +
7E VAL* 1.3 65.9 + - - +
8E ILE* 4.4 1.8 - - + -
31E THR* 3.3 11.7 - - - +
33E ILE* 3.6 33.7 - - + -
88E VAL* 4.2 5.8 - - + -
96E ILE* 4.7 15.7 - - + -
98E TYR* 3.2 34.0 - - + +
100E TYR 3.0 3.6 + - - +
101E LEU* 3.3 24.2 - - + +
102E VAL* 2.9 25.8 + - - -
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Residues in contact with VAL 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E VAL* 4.3 11.4 - - + -
6E VAL* 1.3 78.2 - - - +
8E ILE* 1.3 58.7 + - - +
9E GLY 3.8 6.2 + - - +
14E GLY* 3.4 37.0 - - - +
17E THR* 5.1 0.9 - - - -
18E ALA* 4.2 24.7 - - + +
21E LEU* 4.9 2.2 - - + -
30E ILE* 4.4 5.6 - - + -
31E THR 2.8 14.5 + - - +
32E LEU* 3.4 9.4 - - + -
33E ILE* 2.7 33.8 + - - +
102E VAL* 3.4 25.1 - - + +
104E ALA* 4.9 0.7 - - + -
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Residues in contact with ILE 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E VAL* 4.4 7.4 - - + -
7E VAL* 1.3 75.2 - - - +
9E GLY* 1.3 62.9 + - - +
33E ILE* 3.5 6.5 - - + +
78E ALA* 3.6 26.9 - - + -
81E ILE* 4.0 25.4 - - + -
88E VAL* 4.1 18.2 - - + -
101E LEU* 3.7 27.8 - - + -
102E VAL 2.9 9.2 + - - +
103E ILE* 4.5 7.9 - - + -
104E ALA* 2.8 34.5 + - - +
105E THR* 3.6 22.4 - - + -
259E VAL* 4.8 1.6 - - + -
441E FAD 3.6 9.4 - - + -
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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
------------------------------------------------------------
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