Contacts of the strand formed by residues 69 - 73 (chain C) in PDB entry 4B5G
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 VAL 69 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL 3.3 8.1 - - - +
35C GLN* 3.6 17.7 - - + -
37C LEU* 3.8 4.5 - - - +
58C TRP* 3.3 2.6 - - - +
59C HIS 3.0 28.6 + - - +
68C GLY* 1.3 77.7 - - - +
70C ALA* 1.3 65.6 + - - +
93C GLY 4.4 0.7 - - - +
94C ARG* 3.8 4.7 - - - -
95C PHE 3.4 25.8 - - - +
96C VAL* 3.6 17.9 - - + +
107C SER* 3.5 13.5 - - - +
108C LEU 4.3 0.2 - - - -
109C TYR* 3.5 37.2 - - + +
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C CYS* 3.4 0.3 - - - -
34C VAL* 2.9 48.1 + - + +
37C LEU* 4.4 5.2 - - + -
57C HIS 3.2 13.0 - - - +
58C TRP* 3.8 12.1 - - + +
69C VAL* 1.3 78.8 - - - +
71C VAL* 1.3 63.7 + - - +
72C TYR* 4.0 20.0 - - + +
96C VAL* 4.4 1.6 - - - -
107C SER* 3.3 8.8 + - - -
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ILE* 4.1 15.3 - - + -
32C VAL 3.7 2.7 - - - -
33C CYS* 4.0 8.3 - - - -
55C HIS 4.4 0.3 - - - -
56C GLY* 3.2 2.9 - - - -
57C HIS* 2.9 34.2 + - - +
70C ALA* 1.3 79.4 - - - +
72C TYR* 1.3 74.5 + - - +
73C SER* 5.1 1.4 + - - -
96C VAL* 3.8 15.9 - - + +
98C CYS* 3.7 32.2 - - + -
100C PHE* 4.9 4.7 - - + -
105C VAL* 4.7 5.8 - - + +
106C ILE 4.6 0.9 - - - -
107C SER* 3.5 28.7 - - - +
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Residues in contact with TYR 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ILE* 3.2 20.1 - - + +
16C TYR* 5.4 0.2 - - - -
20C PHE* 5.5 0.2 - + - -
24C ILE* 4.8 8.3 - - + -
31C ILE* 3.3 8.1 - - - +
32C VAL* 2.9 54.4 + - + +
34C VAL* 3.7 32.8 - - + +
37C LEU* 4.4 1.6 - - - +
44C LEU* 5.8 0.3 - - - +
48C MET 3.0 22.3 + - - -
49C LYS* 3.5 21.3 - - - -
51C PRO* 3.6 33.0 - - + -
54C MET* 3.6 17.5 - - + -
55C HIS 3.2 6.7 - - - +
56C GLY* 3.9 9.6 - - - -
57C HIS 5.3 0.4 - - - -
58C TRP* 5.4 2.7 - + - -
70C ALA* 4.0 15.2 - - + +
71C VAL* 1.3 73.2 - - - +
73C SER* 1.3 63.5 + - - +
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Residues in contact with SER 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ASP 3.4 5.8 - - - -
31C ILE* 4.0 10.5 - - - -
54C MET* 3.4 6.7 - - - +
55C HIS* 2.9 34.1 + - - +
71C VAL* 5.1 2.6 + - - +
72C TYR* 1.3 76.7 - - - +
74C LYS* 1.3 61.7 + - - +
75C ARG* 2.7 27.5 + - - +
77C PRO* 3.8 9.2 - - - +
100C PHE* 3.4 28.9 - - - -
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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