Contacts of the strand formed by residues 98 - 103 (chain A) in PDB entry 8CHO
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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ALA* 4.7 7.9 - - + -
80A PHE 3.3 11.2 - - - +
81A ALA* 4.2 18.6 - - + +
97A PRO* 1.3 78.7 - - - +
99A ASP* 1.3 73.1 + - - +
100A HIS* 5.4 1.3 - - + +
113A ARG 4.0 0.7 - - - +
115A LEU* 3.0 40.6 + - + +
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Residues in contact with ASP 99 (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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14A TYR* 3.8 16.8 + - - -
79A ALA* 3.2 7.6 - - - +
80A PHE* 2.9 58.6 + - + -
82A PHE* 3.3 30.1 - - - -
97A PRO* 4.1 1.6 - - - +
98A ILE* 1.3 77.1 - - - +
100A HIS* 1.3 61.6 + - - +
101A PHE* 4.3 4.7 - - + -
112A MET* 3.9 11.4 - - - +
113A ARG 3.4 3.6 - - - +
114A ALA* 3.2 29.4 - - - +
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Residues in contact with HIS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 2.7 30.6 + - + -
78A ALA 3.4 16.6 - - - -
79A ALA* 4.6 8.5 - - + -
98A ILE* 5.4 2.0 - - + +
99A ASP* 1.3 76.1 - - - +
101A PHE* 1.3 68.6 + - - +
102A ARG* 3.8 25.9 + - - -
111A SER* 3.7 2.2 + - - +
112A MET* 3.5 4.5 - - - -
113A ARG* 3.0 52.2 + - + +
115A LEU* 6.5 0.7 - - + -
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Residues in contact with PHE 101 (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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10A VAL* 4.3 11.4 - - + -
11A VAL* 4.2 14.4 - - + -
14A TYR* 3.9 39.7 - + + -
29A LEU* 6.0 0.4 - - + -
30A PHE* 5.2 2.9 - + - -
77A GLU* 3.3 7.2 - - - +
78A ALA* 2.8 32.5 + - + +
80A PHE* 4.0 23.8 - + - -
99A ASP* 4.5 3.4 - - + -
100A HIS* 1.3 85.7 - - - +
102A ARG* 1.3 59.7 + - - +
103A PHE* 3.6 26.5 - + + -
109A VAL* 3.9 27.8 - - + -
111A SER 3.5 3.4 - - - +
112A MET* 3.3 31.9 - - + -
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Residues in contact with ARG 102 (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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76A ASN* 3.3 13.9 - - + +
77A GLU* 3.6 23.6 + - + +
100A HIS* 3.8 23.2 + - + -
101A PHE* 1.3 74.0 - - - +
103A PHE* 1.3 67.1 + - - +
109A VAL* 3.6 3.5 - - - -
110A VAL* 2.9 38.2 + - + +
111A SER* 3.1 35.4 + - - +
113A ARG* 4.9 10.1 - - - +
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Residues in contact with PHE 103 (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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2A ASN* 3.4 19.5 - - - +
6A HIS* 4.4 2.5 - - - -
7A MET* 3.5 54.7 - - + -
10A VAL* 3.7 30.5 - - + -
76A ASN* 2.8 29.6 + - - +
78A ALA* 3.9 9.0 - - + -
101A PHE* 3.6 36.6 - + + -
102A ARG* 1.3 81.5 - - - +
104A ASN* 1.3 63.6 + - - +
107A GLY 3.5 20.2 - - - -
108A LYS 3.2 10.3 - - - +
109A VAL* 4.0 5.2 - - + -
110A VAL* 4.0 6.0 - - - +
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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