Contacts of the strand formed by residues 78 - 83 (chain K) in PDB entry 4M7A
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 78 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26K VAL* 3.9 15.3 - - + -
27K LYS 3.8 3.4 - - - -
28K LEU* 4.0 11.0 - - + -
45K MET* 3.6 33.5 - - + +
47K VAL* 4.8 2.9 - - + -
73K LEU* 4.7 4.9 - - + +
74K ARG 3.5 17.0 - - - +
75K GLY 3.0 15.7 + - - +
76K THR 4.6 2.4 - - - +
77K GLN* 1.3 76.3 - - - +
79K MET* 1.3 63.1 + - - +
80K TYR* 3.8 22.0 - - - +
81K ILE* 4.0 13.5 - - + -
74L SER* 3.5 18.5 + - - -
76L ASN* 5.4 1.7 + - - -
77L ASN* 4.3 5.6 + - - -
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Residues in contact with MET 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K LYS* 2.6 39.5 + - + +
28K LEU 4.1 10.1 - - - +
29K ALA* 4.4 4.5 - - - +
77K GLN 3.4 2.4 + - - -
78K VAL* 1.3 72.4 - - - +
80K TYR* 1.3 68.0 + - + +
24L LEU* 3.1 25.1 - - + -
28L ARG* 3.0 36.1 - - - +
30L PHE* 3.0 38.6 - - + -
73L LEU* 3.5 7.4 - - + +
74L SER* 3.0 28.8 + - - +
77L ASN* 4.3 13.9 + - - +
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Residues in contact with TYR 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K ASN* 3.9 12.1 - - + -
26K VAL* 3.2 10.6 - - - +
27K LYS* 2.9 58.5 + - + +
33K LEU* 5.4 3.2 - - + +
57K GLU 4.8 0.3 + - - -
78K VAL* 4.0 2.9 - - - -
79K MET* 1.3 90.0 - - + +
81K ILE* 1.3 64.1 + - - +
82K SER* 3.8 17.7 - - - -
30L PHE* 3.5 32.8 - + - -
50L GLU* 2.7 33.2 + - - -
65L MET* 4.1 7.1 - - - -
67L HIS* 3.3 25.2 - + - -
71L MET* 3.9 9.6 - - + -
72L LEU 3.4 12.8 - - - +
73L LEU* 3.7 8.5 - - + -
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Residues in contact with ILE 81 (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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15K PHE* 4.0 7.4 - - + -
19K ILE* 4.1 17.9 - - + -
24K VAL* 4.0 22.7 - - + -
25K ASN 3.5 2.7 - - - -
26K VAL* 4.1 13.0 - - + -
38K LEU* 4.5 5.4 - - + -
41K ILE* 3.5 32.5 - - + -
45K MET* 4.5 12.6 - - + -
47K VAL* 3.6 17.3 - - + -
78K VAL* 4.0 10.5 - - + -
80K TYR* 1.3 77.7 - - - +
82K SER* 1.3 59.7 + - - +
71L MET* 3.7 0.9 - - - -
72L LEU* 3.0 46.0 + - + +
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Residues in contact with SER 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K PHE* 5.9 0.4 - - - -
24K VAL* 3.2 8.6 - - - +
25K ASN* 2.9 41.7 + - - -
80K TYR* 3.8 15.5 - - - -
81K ILE* 1.3 74.7 - - - +
83K GLU* 1.3 66.0 + - - +
67L HIS* 2.8 37.4 + - - +
69L GLY 6.0 0.2 - - - -
70L ARG 3.7 5.3 + - - -
71L MET* 3.7 13.3 - - - +
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Residues in contact with GLU 83 (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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15K PHE* 5.7 0.4 - - + -
19K ILE* 4.3 22.1 - - + +
22K LYS* 5.3 9.3 - - + +
23K THR 3.9 9.4 - - - +
24K VAL* 4.3 7.4 - - + -
25K ASN* 5.1 0.7 - - - -
82K SER* 1.3 80.2 + - - +
84K GLN* 1.3 69.0 + - - +
68L HIS 2.8 18.6 - - - +
69L GLY* 3.2 13.8 - - - -
70L ARG* 3.0 55.9 + - - +
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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