Contacts of the strand formed by residues 100 - 105 (chain O) in PDB entry 5C7O
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 LYS 100 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75O GLU* 3.6 35.2 - - - +
76O LEU 4.0 14.7 + - - +
77O THR* 3.4 7.6 - - + -
78O VAL* 3.0 25.8 + - - +
98O GLY 3.7 3.8 + - - +
99O VAL* 1.3 73.0 - - - +
101O VAL* 1.3 60.7 + - - +
102O VAL* 3.9 16.8 + - + -
143O HIS* 3.8 32.6 + - + +
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Residues in contact with VAL 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O VAL* 3.4 17.0 - - + +
80O ILE* 4.2 15.5 - - + -
91O LEU* 3.7 26.2 - - + -
94O CYS* 3.6 39.0 - - + -
95O MET* 5.7 1.1 - - - -
99O VAL 3.4 1.8 + - - +
100O LYS* 1.3 73.2 - - - +
102O VAL* 1.3 60.3 + - - +
103O ALA 3.9 16.6 - - - +
104O VAL* 4.3 2.2 - - + -
143O HIS* 2.4 37.7 + - + +
145O ILE* 3.5 18.0 - - + +
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Residues in contact with VAL 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77O THR* 3.9 24.7 - - + -
78O VAL 2.9 18.6 + - - +
100O LYS* 4.2 14.8 - - + -
101O VAL* 1.3 76.2 - - - +
103O ALA* 1.3 64.0 + - + +
143O HIS* 4.6 4.0 - - + -
144O GLU 4.7 2.3 - - - +
145O ILE* 3.9 4.6 - - - -
146O SER* 3.0 23.4 + - - -
161O VAL* 3.9 39.0 - - + +
164O PRO* 3.9 19.1 - - + -
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Residues in contact with ALA 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O VAL 3.6 0.2 + - - -
79O GLY* 3.3 4.0 - - - -
80O ILE 2.9 23.0 + - - -
101O VAL* 3.6 4.7 - - - +
102O VAL* 1.3 85.1 - - + +
104O VAL* 1.3 67.5 - - - +
145O ILE* 3.7 2.9 - - - +
146O SER* 3.2 14.4 - - - +
148O TYR* 3.8 27.8 - - + -
158O TRP* 4.0 14.1 - - + -
161O VAL* 4.1 9.2 - - + -
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Residues in contact with VAL 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80O ILE* 3.3 23.6 - - + +
83O PHE* 3.5 43.3 - - + -
91O LEU* 4.9 2.2 - - + -
101O VAL* 4.3 7.4 - - + -
103O ALA* 1.3 81.8 - - - +
105O ASN* 1.3 64.7 - - - +
114O MET* 3.6 22.9 - - + -
138O LEU* 4.9 6.5 - - + -
145O ILE* 3.9 15.3 - - + -
146O SER 2.9 7.3 + - - +
147O VAL* 3.4 7.8 - - + +
148O TYR* 2.9 24.0 + - - +
158O TRP* 5.3 0.4 - - - -
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Residues in contact with ASN 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80O ILE 2.8 11.6 + - - +
81O ASN* 2.8 27.2 + - - +
82O GLY 2.9 28.8 + - - -
104O VAL* 1.3 76.5 - - - +
106O ASP* 1.3 62.7 + - - +
148O TYR* 3.1 21.6 - - + +
150O CYS* 2.7 53.5 + - - +
151O LYS 5.4 0.4 - - - -
156O ILE* 3.4 26.9 - - + +
158O TRP* 4.5 3.5 - - + -
501O NAD 3.8 3.8 + - - -
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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