Contacts of the strand formed by residues 70 - 73 (chain A) in PDB entry 3EHW
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 ILE 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A PHE* 4.1 20.0 - - + -
29A ALA 3.3 9.6 - - - +
30A ARG* 4.5 1.6 - - - -
31A LEU* 4.0 4.3 - - - -
35A ALA* 3.5 18.4 - - + -
36A THR 4.5 10.3 - - - +
38A PRO* 3.7 30.7 - - + -
50A LEU* 4.4 12.8 - - + -
68A THR* 3.1 20.0 - - - +
69A ASP* 1.3 85.3 - - - +
71A GLN* 1.3 59.0 + - - +
72A ILE* 3.8 25.1 - - + -
108A ASN* 3.5 2.3 - - - -
109A VAL* 2.9 30.7 + - + +
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Residues in contact with GLN 71 (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 PHE* 3.1 6.8 - - - +
29A ALA* 3.0 54.0 + - + +
31A LEU* 3.8 22.8 - - + +
70A ILE* 1.3 74.5 - - - +
72A ILE* 1.3 62.6 + - - +
106A ARG* 2.9 25.9 - - - +
107A GLY 3.5 19.5 - - - +
109A VAL* 4.6 0.2 - - - -
146B GLN 4.9 0.8 + - - -
147B ALA* 4.5 3.6 - - - +
148B LEU* 3.6 33.5 + - + +
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Residues in contact with ILE 72 (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 LEU* 4.2 9.2 - - + -
27A ARG 3.4 5.2 - - - +
28A PHE* 3.9 9.0 - - + -
38A PRO* 6.0 0.7 - - + -
70A ILE* 3.8 25.4 - - + -
71A GLN* 1.3 79.6 - - - +
73A ALA* 1.3 59.4 + - - +
74A LEU* 3.8 26.0 + - + +
101A ILE* 3.9 23.3 - - + -
102A ASP 5.6 0.3 - - - +
105A TYR* 3.1 25.1 + - + +
106A ARG* 3.5 2.9 + - - -
107A GLY 4.6 1.0 + - - -
109A VAL* 3.9 19.0 - - + +
132A LEU* 3.6 34.5 - - + -
148B LEU* 3.4 8.6 - - - +
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Residues in contact with ALA 73 (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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25A GLN 3.8 4.0 - - - +
26A LEU* 3.9 2.8 - - - +
27A ARG* 2.8 39.5 + - + +
72A ILE* 1.3 72.7 - - - +
74A LEU* 1.3 66.1 + - - +
75A PRO 3.7 1.2 - - - -
106A ARG* 3.9 25.6 - - - +
148B LEU* 3.7 22.0 - - + +
149B ASP* 4.4 4.9 - - - +
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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