Contacts of the strand formed by residues 33 - 38 (chain K) in PDB entry 6A3W
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 ALA 33 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K ILE* 4.6 2.5 - - + -
32K TYR* 1.3 72.3 - - - +
34K HIS* 1.3 62.2 + - - +
35K TRP* 4.5 10.6 - - + +
48K ILE* 4.5 0.3 - - - +
49K TYR 4.0 0.7 - - - -
50K GLN 3.4 2.9 + - - -
51K ASP* 2.4 55.6 + - - +
66K ASN* 3.8 11.9 - - - +
71K ALA* 3.9 22.7 - - + -
88K CYS* 5.7 1.6 - - + -
89K ALA 3.5 6.3 - - - +
90K THR* 4.0 11.0 - - + -
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Residues in contact with HIS 34 (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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101J GLY* 3.2 29.7 + - - -
102J ILE* 3.4 28.3 - - + +
32K TYR* 3.9 27.3 + + + +
33K ALA* 1.3 73.7 - - - +
35K TRP* 1.3 64.6 + - - +
36K TYR* 3.9 20.4 - - + +
46K LEU* 4.4 2.2 - - + -
48K ILE 3.3 9.0 - - - +
49K TYR* 3.5 6.0 - - + +
50K GLN* 3.0 33.0 + - + -
87K TYR 3.7 0.7 - - - +
88K CYS* 3.3 4.2 - - - +
89K ALA* 2.8 44.8 + - + +
90K THR* 4.9 2.7 - - - -
91K TYR* 5.2 3.2 + - - +
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Residues in contact with TRP 35 (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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7K GLN* 3.9 6.3 - - - -
21K ILE* 3.5 38.4 - - + -
22K THR 4.0 1.1 - - - -
23K CYS* 3.7 24.9 - - + -
33K ALA* 4.5 7.0 - - - +
34K HIS* 1.3 79.0 - - - +
36K TYR* 1.3 61.4 + - - +
46K LEU* 3.6 3.5 - - - +
47K VAL* 2.8 36.1 + - + -
48K ILE* 2.8 43.7 + - + +
51K ASP* 5.3 3.3 + - - +
64K GLY* 5.5 0.4 - - - -
65K SER 5.1 1.4 + - - -
71K ALA* 3.8 24.4 - - + +
72K THR 4.0 5.2 + - - +
73K LEU* 3.6 44.7 - - + +
86K TYR* 4.5 2.7 - - + -
87K TYR 3.4 10.3 - - - -
88K CYS* 3.8 28.9 - - + -
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Residues in contact with TYR 36 (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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45J LEU* 5.1 2.5 - - + -
101J GLY 3.4 8.3 + - - -
102J ILE* 3.7 0.3 - - - -
103J PHE* 2.8 62.1 + + + -
106J TRP* 3.9 17.3 - + - -
34K HIS* 3.9 12.1 - - + +
35K TRP* 1.3 75.0 - - - +
37K GLN* 1.3 59.9 + - - +
44K PRO* 4.2 13.0 - - + -
45K VAL 3.3 5.4 - - - +
46K LEU* 3.5 37.0 - - + +
47K VAL* 4.6 0.2 - - - -
85K ASP 3.7 0.9 - - - +
86K TYR* 3.3 9.4 - - - +
87K TYR* 2.8 48.4 + - + +
89K ALA* 3.8 23.3 - - + -
100K PHE* 4.0 14.8 - + - -
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Residues in contact with GLN 37 (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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35K TRP 4.3 0.2 + - - -
36K TYR* 1.3 74.3 - - - +
38K GLN* 1.3 63.7 + - - +
39K LYS* 4.3 15.2 - - + +
43K SER 4.2 0.9 - - - +
44K PRO* 3.4 1.1 - - - +
45K VAL* 2.7 48.8 + - - +
47K VAL* 3.6 20.4 - - + +
58K ILE* 6.1 0.3 - - - +
62K PHE* 3.9 13.7 - - - -
81K MET 4.4 4.2 + - - -
82K ASP* 4.2 12.1 + - - +
84K ALA* 3.6 18.3 - - + +
85K ASP 3.5 3.6 - - - -
86K TYR* 2.8 37.9 + - + -
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Residues in contact with GLN 38 (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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39J GLN* 2.8 44.7 + - - -
45J LEU* 4.2 0.9 - - - +
95J TYR* 3.3 14.8 + - - -
37K GLN* 1.3 76.6 - - - +
39K LYS* 1.3 62.5 + - - +
40K PRO* 4.8 0.5 - - - +
42K GLN 3.2 28.0 + - - +
43K SER 4.6 1.3 - - - -
44K PRO* 3.9 23.7 - - + +
84K ALA* 3.8 3.5 - - - -
85K ASP* 2.9 45.0 + - - +
87K TYR* 3.5 18.6 + - + -
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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