Contacts of the strand formed by residues 69 - 74 (chain i) in PDB entry 5MQF
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 i).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21i VAL* 5.9 5.4 - - + -
22i LYS 4.0 6.3 - - - +
23i LEU* 4.5 1.3 - - - +
24i LYS* 5.3 1.4 - - - +
40i MET 5.1 6.1 - - - +
64i ILE* 6.3 2.2 - - + -
65i ARG 4.0 2.3 + - - +
66i CYS* 3.1 19.2 + - - +
67i ASN 4.1 5.2 - - - +
68i ASN* 1.3 77.9 - - - +
70i LEU* 1.3 64.4 + - - +
71i TYR* 4.8 4.0 - - - +
80j LYS* 3.9 16.6 - - + +
82j ASP* 5.1 5.5 - - - +
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Residues in contact with LEU 70 (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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22i LYS* 3.0 19.2 + - + +
23i LEU 3.9 3.4 - - - +
24i LYS* 3.8 21.5 - - + +
68i ASN 3.4 2.8 + - - -
69i VAL* 1.3 73.5 - - - +
71i TYR* 1.3 63.6 + - + +
79j LEU* 3.8 1.9 - - - +
80j LYS* 3.0 30.9 + - - +
83j ASN* 5.4 13.8 - - + +
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Residues in contact with TYR 71 (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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21i VAL* 3.5 3.4 - - - +
22i LYS* 3.0 33.3 + - + +
69i VAL* 3.9 4.6 - - - +
70i LEU* 1.3 82.9 - - + +
72i ILE* 1.3 64.1 + - - +
77j ILE* 5.3 6.3 - - + -
78j MET 3.2 17.0 - - - +
79j LEU* 4.0 10.3 - - + -
80j LYS 4.6 0.2 - - - +
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Residues in contact with ILE 72 (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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19i VAL* 5.7 5.6 - - + -
20i MET 3.7 6.1 - - - +
21i VAL* 4.4 8.1 - - + +
71i TYR* 1.3 75.5 - - - +
73i ARG* 1.3 61.1 + - - +
76j ARG 3.7 0.7 - - - +
77j ILE* 3.5 5.4 - - - +
78j MET* 3.0 39.8 + - + +
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Residues in contact with ARG 73 (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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19i VAL* 3.2 7.9 - - - +
20i MET* 2.8 46.1 + - + +
72i ILE* 1.3 76.3 - - - +
74i GLY* 1.3 67.3 + - - +
75i VAL* 6.0 0.9 - - + -
74j LEU* 4.6 15.0 - - + +
76j ARG 3.5 10.3 - - - +
77j ILE* 5.4 2.0 - - + -
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Residues in contact with GLY 74 (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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14i LEU* 5.8 8.5 - - - +
17i LYS* 6.3 0.9 - - - -
18i PRO 3.7 8.5 - - - -
19i VAL* 4.3 2.9 - - - -
73i ARG* 1.3 80.3 - - - +
75i VAL* 1.3 61.2 + - - +
74j LEU 4.8 6.2 - - - +
76j ARG* 3.7 16.0 + - - +
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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