Contacts of the strand formed by residues 66 - 69 (chain I) in PDB entry 3H1J
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 66 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ARG* 3.6 34.7 - - - +
99B TYR* 3.2 1.5 - - - -
100B SER 2.8 36.2 + - - +
176B LEU* 3.8 16.7 - - + +
177B TYR* 3.4 25.6 - - + +
65I VAL* 1.3 72.9 - - - +
67I GLY* 1.3 59.8 + - - +
75I SER 4.0 1.8 - - - +
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Residues in contact with GLY 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ARG* 5.0 0.2 - - - -
98B VAL 3.3 6.3 - - - -
99B TYR* 3.8 15.5 - - - -
65I VAL* 4.0 1.6 + - - +
66I ALA* 1.3 75.2 - - - +
68I ILE* 1.3 69.8 + - - +
69I SER* 5.3 0.9 - - - -
73I PRO 5.3 0.7 - - - -
74I ALA* 4.4 0.3 - - - +
75I SER* 3.1 49.3 + - - +
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Residues in contact with ILE 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A THR* 4.8 10.5 - - - +
285A GLY* 5.6 2.9 - - - -
70B ARG* 3.9 29.4 - - + +
71B LEU* 3.1 35.0 - - + -
73B SER* 4.5 5.8 - - - +
74B PRO* 6.1 0.2 - - + -
97B SER* 3.2 2.3 - - - -
98B VAL* 2.6 44.5 + - - +
99B TYR* 5.2 0.6 - - - -
147B ASP* 3.2 26.5 - - + +
67I GLY* 1.3 81.1 - - - +
69I SER* 1.3 78.7 + - - +
73I PRO 4.9 1.1 - - - -
74I ALA* 4.2 13.2 - - + -
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Residues in contact with SER 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A THR 3.8 4.1 + - - +
285A GLY* 2.9 22.3 + - - -
73B SER* 5.5 2.6 + - - -
96B LEU 3.5 4.7 - - - -
97B SER* 3.3 19.6 + - - +
99B TYR* 5.8 1.4 - - - -
67I GLY 5.3 0.3 - - - -
68I ILE* 1.3 88.6 + - - +
70I LEU* 1.3 60.5 + - - +
71I ASN* 4.1 0.9 - - - -
72I ALA* 3.3 42.5 + - - +
73I PRO 3.5 11.6 + - - -
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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