Contacts of the strand formed by residues 97 - 103 (chain A) in PDB entry 5ODS
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 SER 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A PHE* 3.5 5.1 - - - -
92A ASN* 2.8 33.0 + - - +
95A MET* 3.0 24.9 - - - +
96A LYS* 1.3 77.9 - - - +
98A LYS* 1.3 63.2 + - - +
99A MET* 5.6 0.7 - - - +
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Residues in contact with LYS 98 (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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89A GLN* 3.4 38.0 - - + +
90A ILE 4.2 0.9 - - - -
91A PHE* 3.9 14.1 - - + -
97A SER* 1.3 73.7 - - - +
99A MET* 1.3 65.8 + - - +
100A LYS 3.7 17.0 - - - +
101A ALA* 4.2 14.5 - - + +
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Residues in contact with MET 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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79A VAL* 3.6 35.4 - - + -
90A ILE* 2.9 22.8 + - + +
92A ASN* 3.9 33.2 - - + +
97A SER* 3.6 1.3 + - - +
98A LYS* 1.3 76.5 - - - +
100A LYS* 1.3 68.6 + - + +
132A MET* 3.7 44.9 - - + +
133A GLU* 5.5 1.1 - - - +
134A GLY 5.5 0.2 - - - +
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Residues in contact with LYS 100 (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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89A GLN* 3.6 2.8 - - - -
90A ILE* 3.1 33.0 + - + +
98A LYS* 3.7 9.0 - - - +
99A MET* 1.3 83.8 - - - +
101A ALA* 1.3 68.4 + - - +
130A TRP* 3.3 22.4 - - + +
131A SER 3.2 27.4 - - - +
132A MET* 3.5 21.3 - - - +
133A GLU 3.9 1.1 - - - -
134A GLY 3.2 26.9 - - - +
135A GLU* 3.8 8.0 + - - +
136A SER 2.9 33.7 + - - +
137A GLN* 4.5 6.1 + - - -
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A THR* 5.9 2.9 - - + -
88A LEU 3.4 12.1 - - - +
89A GLN* 4.8 0.9 - - + -
98A LYS* 4.2 23.6 - - + +
100A LYS* 1.3 82.1 + - - +
102A HIS* 1.3 67.2 + - - +
130A TRP* 3.7 6.7 - - - -
137A GLN* 4.4 7.3 - - - +
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Residues in contact with HIS 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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86A LYS 3.8 0.3 - - - +
87A THR* 4.6 1.5 - - - +
88A LEU* 2.6 46.8 + - + +
101A ALA* 1.3 75.3 - - - +
103A THR* 1.3 79.7 + - - +
104A MET* 3.6 31.2 - - + +
121A LEU* 5.8 0.4 - - - +
130A TRP* 3.7 21.4 - - + -
137A GLN* 3.3 43.8 + - + +
138A PRO* 3.4 19.0 - - + +
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Residues in contact with THR 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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86A LYS* 3.3 13.9 - - + +
87A THR* 3.8 23.3 + - - +
102A HIS* 1.3 89.6 + - - +
104A MET* 1.3 68.7 - - - +
105A THR* 4.0 1.2 + - - +
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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
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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