Contacts of the strand formed by residues 72 - 79 (chain K) in PDB entry 2DYY
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 72 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58K ILE* 5.5 0.2 - - + -
62K LEU* 3.7 26.7 - - + -
69K LEU 3.6 11.2 - - - +
70K ASN 3.4 1.0 - - - -
71K ASP* 1.3 76.7 - - - +
73K ILE* 1.3 61.6 + - - +
74K LYS 3.8 7.4 - - - +
75K VAL* 3.3 32.5 - - + -
96K PHE* 3.6 23.1 - - + -
99K SER* 3.6 4.5 + - - -
101K PRO* 3.3 24.7 - - + +
121K ALA* 4.7 8.7 - - + -
122K ILE 3.5 7.2 - - - +
123K ALA* 3.9 6.5 - - + +
2L LYS* 3.4 13.5 - - - -
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Residues in contact with ILE 73 (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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26K PHE* 3.5 22.9 - - + -
71K ASP 3.5 13.7 - - - +
72K VAL* 1.3 74.0 - - - +
74K LYS* 1.3 65.6 + - + +
101K PRO* 3.5 7.0 - - - +
102K ALA* 3.0 23.9 + - - +
122K ILE* 2.9 24.4 + - + +
124K TYR* 3.7 14.8 - - + -
2L LYS* 3.9 18.2 - - + -
21L ILE* 3.9 22.5 - - + +
23L ALA* 3.5 14.1 - - + -
28L PHE* 3.4 38.8 - - + +
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Residues in contact with LYS 74 (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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72K VAL* 3.6 0.8 - - - +
73K ILE* 1.3 88.2 - - + +
75K VAL* 1.3 70.2 + - - +
76K THR* 2.8 29.9 + - - -
102K ALA* 3.3 18.6 - - + +
104K VAL* 3.7 10.2 - - - +
120K GLU* 5.2 3.4 + - - +
121K ALA* 3.4 0.5 - - - -
122K ILE* 3.0 48.1 + - + +
28L PHE* 3.9 31.9 - - + -
29L ILE 5.1 5.6 - - - +
120L GLU* 3.0 37.2 + - - -
121L ALA 5.9 0.4 - - - -
122L ILE* 5.3 7.9 - - + -
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Residues in contact with VAL 75 (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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72K VAL* 3.3 30.5 - - + -
74K LYS* 1.3 76.7 + - - +
76K THR* 1.3 71.0 + - - +
77K VAL* 4.1 9.0 - - + -
92K TYR* 3.8 25.6 - - + +
96K PHE* 3.9 19.1 - - + -
101K PRO* 4.1 3.8 - - + -
102K ALA 2.9 8.9 + - - +
103K ARG* 3.3 4.4 - - + +
104K VAL 3.0 22.7 + - - -
119K ILE* 3.5 21.1 - - + -
120K GLU 3.4 11.2 - - - +
121K ALA* 4.2 6.5 - - + -
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Residues in contact with THR 76 (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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74K LYS* 2.8 29.8 + - - -
75K VAL* 1.3 73.8 - - - +
77K VAL* 1.3 66.8 + - - +
78K TYR* 3.4 37.5 - - + +
104K VAL* 3.3 22.9 - - + +
106K VAL* 5.7 0.4 - - + -
118K GLU 3.9 0.5 - - - +
119K ILE* 3.4 5.5 - - - +
120K GLU* 2.9 52.9 + - - +
78L TYR* 4.4 4.0 - - - +
120L GLU* 4.5 2.0 + - - +
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Residues in contact with VAL 77 (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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75K VAL* 4.1 15.5 - - + -
76K THR* 1.3 76.7 - - - +
78K TYR* 1.3 66.2 - - - +
79K LEU* 4.0 13.7 - - + -
88K MET* 4.0 32.1 - - + -
92K TYR* 4.6 3.1 - - + -
103K ARG* 4.5 10.1 - - + -
104K VAL 2.7 16.1 + - - +
105K ALA* 3.5 8.2 - - + -
106K VAL* 3.0 28.6 + - - +
117K ILE* 3.9 28.3 - - + -
118K GLU 3.8 2.5 - - - -
119K ILE* 4.4 10.8 - - + -
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Residues in contact with TYR 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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76J THR* 4.6 4.2 - - + +
78J TYR* 4.0 19.1 + + - -
104J VAL* 3.7 24.0 - - + +
106J VAL* 4.3 15.7 - - + -
76K THR* 3.4 33.7 - - + +
77K VAL* 1.3 73.4 - - - +
79K LEU* 1.3 61.6 + - - +
106K VAL* 3.5 26.9 - - + -
108K VAL* 3.7 13.5 - - + -
111K LEU* 3.2 27.4 - - + +
117K ILE* 3.3 4.0 - - - +
118K GLU* 3.0 52.3 + - + +
120K GLU* 3.9 15.3 + - + -
78L TYR* 4.2 9.2 + + - -
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Residues in contact with LEU 79 (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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47K ILE* 3.8 29.2 - - + -
77K VAL* 4.0 10.1 - - + -
78K TYR* 1.3 73.8 - - - +
80K LYS* 1.3 61.6 + - - +
81K ASP 3.9 3.6 - - - +
84K ASP* 3.9 5.2 - - - -
85K PHE* 3.3 45.8 - - + +
88K MET* 4.5 13.5 - - + -
105K ALA* 5.8 2.7 - - + -
106K VAL 3.1 12.7 + - - +
107K GLU* 3.4 7.0 - - + +
108K VAL* 2.8 34.4 + - - +
111K LEU* 4.4 0.4 - - - -
116K LEU 3.5 5.6 - - - +
117K ILE* 3.8 25.4 - - + -
110L ARG* 4.6 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