Contacts of the strand formed by residues 100 - 102 (chain U) in PDB entry 3HOU
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 PHE 100 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U GLU* 3.2 51.1 - - + -
55U THR* 3.1 25.4 - - + -
84U VAL 4.5 0.2 - - - +
85U PHE* 3.0 21.8 - - - +
86U PHE* 3.2 31.7 + + + -
88U SER* 4.2 16.2 - - - -
98U VAL* 3.5 26.5 - - + -
99U LEU* 1.3 82.0 - - - +
101U PHE* 1.3 63.4 + - - +
102U VAL* 5.1 0.6 - - + +
109U ILE* 4.7 8.5 - - + -
110U PHE 3.5 7.2 - - - +
111U THR* 4.1 13.2 - - + -
118U ARG* 4.4 16.4 - - - -
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Residues in contact with PHE 101 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71U SER* 3.2 28.3 - - - -
73U ARG* 2.9 49.6 - - - -
83U ASN* 3.6 19.5 - - + +
85U PHE* 3.9 20.0 - + + -
99U LEU* 3.5 38.4 - - + -
100U PHE* 1.3 76.9 - - - +
102U VAL* 1.3 73.4 + - - +
108U HIS 4.2 1.6 - - - -
109U ILE* 3.4 3.6 - - - +
110U PHE* 2.7 56.3 + + + +
111U THR 4.3 0.4 - - - -
112U SER* 3.7 10.5 - - - -
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Residues in contact with VAL 102 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58U VAL* 4.1 22.2 - - + -
62U ILE* 4.3 22.0 - - + -
82U GLU 3.5 5.2 - - - +
83U ASN* 3.7 4.2 + - - -
84U VAL* 3.5 30.7 + - + +
86U PHE* 5.0 9.6 - - + -
100U PHE 5.1 1.1 - - - +
101U PHE* 1.3 83.6 - - - +
103U CYS* 1.3 75.5 + - - +
104U LEU* 3.3 16.4 + - + +
107U SER* 4.1 20.0 - - - +
108U HIS 3.8 2.9 - - - +
109U ILE* 4.1 13.2 - - + -
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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
------------------------------------------------------------
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