Contacts of the strand formed by residues 60 - 66 (chain K) in PDB entry 5M5X
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 60 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710A SER 5.9 0.4 - - - -
711A LYS* 3.4 29.2 + - - -
53K ALA 5.3 0.4 - - - -
54K THR* 3.3 3.8 + - - -
55K SER* 2.7 37.9 + - - -
58K GLY* 3.1 2.1 - - - -
59K THR* 1.3 81.4 + - - +
61K ALA* 1.3 58.6 + - - +
104K ARG* 3.4 23.1 - - - -
105K ILE 3.8 4.5 - - - -
106K GLN* 3.3 23.4 + - - +
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Residues in contact with ALA 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K LEU* 6.0 0.7 - - + -
54K THR* 3.3 25.6 - - - +
58K GLY 4.9 1.8 - - - +
60K SER* 1.3 75.9 - - - +
62K SER* 1.3 58.3 - - - +
63K PHE* 4.1 20.9 - - + -
104K ARG* 3.4 13.3 - - - +
105K ILE* 3.0 34.2 + - - +
113K ALA* 4.2 16.4 - - + -
114K VAL* 6.2 0.4 - - + -
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Residues in contact with SER 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A TYR* 4.0 16.7 + - - -
703A GLU* 4.3 14.2 + - - +
49K LEU* 5.1 0.7 - - - +
50K LEU* 3.4 24.8 + - - +
53K ALA* 3.3 18.4 - - - +
54K THR* 4.5 5.8 - - - +
61K ALA* 1.3 72.2 - - - +
63K PHE* 1.3 71.6 + - - +
102K ASN* 6.0 0.9 - - - -
103K ILE 3.8 4.0 - - - -
104K ARG* 2.4 36.6 + - - +
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Residues in contact with PHE 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C ILE* 6.1 0.7 - - + -
47K ILE* 4.3 9.2 - - + -
48K LYS 4.4 0.9 - - - -
49K LEU* 3.6 35.7 - - + -
50K LEU* 4.0 4.0 - - - -
61K ALA* 4.1 16.4 - - + -
62K SER* 1.3 85.2 - - - +
64K GLN* 1.3 61.3 + - - +
65K ILE* 4.0 14.6 - - + -
102K ASN* 3.2 9.5 + - - +
103K ILE* 2.9 39.0 + - + +
105K ILE* 3.6 26.9 - - + -
114K VAL* 3.6 30.3 - - + -
117K LEU* 3.6 42.2 - - + -
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Residues in contact with GLN 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K LYS 3.7 1.2 - - - +
47K ILE* 3.7 0.2 - - - +
48K LYS* 3.0 66.3 + - + +
50K LEU* 3.5 25.2 - - + +
63K PHE* 1.3 74.4 - - - +
65K ILE* 1.3 68.4 + - - +
66K VAL* 5.1 5.9 - - + +
100K LEU* 3.7 38.9 - - + +
101K LEU 3.6 4.7 - - - +
102K ASN* 3.7 19.3 - - - +
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Residues in contact with ILE 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C LEU* 4.4 18.8 - - + -
46K LYS* 3.3 22.0 - - - +
47K ILE* 3.7 16.6 - - + -
63K PHE* 4.0 19.5 - - + -
64K GLN* 1.3 82.3 - - - +
66K VAL* 1.3 74.6 - - - +
68K GLU* 3.6 19.9 - - + +
72K LEU* 5.6 1.1 - - + -
100K LEU 3.8 0.2 - - - -
101K LEU* 2.9 39.8 + - + +
103K ILE* 3.7 34.8 - - + -
117K LEU* 5.9 2.9 - - + -
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Residues in contact with VAL 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K GLU* 3.3 36.1 - - + +
46K LYS* 3.0 33.7 + - + +
48K LYS* 6.3 4.3 - - + +
64K GLN* 5.1 7.2 - - + +
65K ILE* 1.3 74.5 - - - +
67K GLU* 1.3 82.7 + - + +
68K GLU* 3.1 4.5 + - - +
99K ASN 4.0 6.5 - - - +
100K LEU* 3.7 22.2 - - + -
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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