Contacts of the strand formed by residues 77 - 82 (chain K) in PDB entry 3QUM
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 THR 77 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21K SER* 5.6 2.1 - - - -
22K CYS 3.6 6.5 - - - -
23K LYS* 3.3 41.1 - - + -
29K ILE* 3.7 4.7 - - - +
72K ASP 3.2 14.2 + - - +
75K SER* 2.6 35.0 + - - +
76K SER* 1.3 78.6 - - - +
78K ALA* 1.3 59.7 + - - +
79K TYR* 2.9 40.1 + - - -
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Residues in contact with ALA 78 (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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21K SER* 3.6 1.4 - - - -
22K CYS* 2.9 41.0 + - - +
29K ILE* 4.2 12.0 - - + +
34K MET* 4.5 24.0 - - + -
36K TRP* 4.1 7.7 - - + +
51K ILE* 5.8 2.7 - - + -
52K PRO* 5.6 3.6 - - + -
70K THR 3.7 8.5 - - - +
71K VAL* 4.3 13.7 - - + +
77K THR* 1.3 72.1 - - - +
79K TYR* 1.3 64.5 + - - +
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Residues in contact with TYR 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K LYS* 4.0 32.1 - - + -
20K ILE 3.3 7.9 - - - +
21K SER* 4.2 20.4 - - - -
36K TRP* 4.1 7.2 + - - -
51K ILE* 5.9 0.2 - - - +
69K LEU* 3.6 5.0 - - - +
70K THR* 2.6 60.3 + - - +
71K VAL* 4.1 1.1 - - - -
72K ASP* 3.7 21.0 + - + +
75K SER* 3.7 10.6 + - - -
77K THR* 2.9 38.0 + - - -
78K ALA* 1.3 73.3 - - - +
80K MET* 1.3 62.4 + - - +
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Residues in contact with MET 80 (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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18K VAL 4.8 0.2 - - - -
19K LYS* 3.8 2.1 - - - -
20K ILE* 3.0 37.7 + - + +
36K TRP* 3.5 53.4 - - + -
48K ILE* 4.0 10.8 - - + -
67K ALA* 4.6 9.2 - - - -
68K THR 3.5 3.8 - - - +
69K LEU* 3.2 27.8 - - + -
79K TYR* 1.3 76.1 - - - +
81K GLN* 1.3 62.3 + - - +
82K LEU* 3.4 32.4 + - + +
90K TYR* 3.9 33.4 - - + -
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Residues in contact with GLN 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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17K SER* 3.5 14.7 + - - -
18K VAL 3.4 11.1 - - - +
19K LYS* 4.5 25.8 - - + +
66K LYS 3.9 0.2 - - - +
67K ALA* 3.4 2.6 - - - -
68K THR* 2.7 57.3 + - - +
70K THR* 5.3 2.1 + - - +
80K MET* 1.3 72.6 - - - +
82K LEU* 1.3 82.3 + - + +
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Residues in contact with LEU 82 (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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17K SER* 3.3 13.3 + - - -
18K VAL* 3.4 22.4 + - + +
20K ILE* 5.9 5.2 - - + -
48K ILE* 6.1 0.4 - - + -
66K LYS* 3.4 14.6 - - + +
67K ALA* 4.1 12.3 - - + -
80K MET* 3.4 31.0 - - + +
81K GLN* 1.3 90.3 - - - +
82K SER* 1.3 72.9 + - - +
86K ASP* 5.1 2.0 - - + -
90K TYR* 3.5 41.7 - - + +
109K VAL* 5.8 4.0 - - + -
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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