Contacts of the strand formed by residues 72 - 79 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LYS* 5.4 1.0 - - - +
21A ILE* 4.7 0.2 - - - +
29C ILE* 6.1 0.7 - - + -
58C ILE* 5.4 0.4 - - + -
62C LEU* 3.8 32.1 - - + -
68C SER 4.4 0.4 - - - +
69C LEU* 3.7 16.8 - - - +
70C ASN 3.5 1.1 - - - +
71C ASP* 1.3 75.5 - - - +
73C ILE* 1.3 60.8 + - - +
74C LYS 3.9 2.2 - - - +
75C VAL* 3.5 22.0 - - + -
96C PHE* 3.9 15.5 - - + -
99C SER* 3.2 17.1 - - - +
101C PRO* 3.2 32.3 - - + +
121C ALA* 4.6 10.5 - - + -
122C ILE 3.4 11.9 - - - +
123C ALA* 3.9 2.7 - - + +
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Residues in contact with ILE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS* 4.2 13.9 - - + -
21A ILE* 3.3 35.1 - - + +
23A ALA* 3.8 8.1 - - + -
28A PHE* 3.6 22.7 - - + +
26C PHE* 3.6 31.6 - - + -
71C ASP 3.3 14.8 - - - +
72C VAL* 1.3 74.1 - - - +
74C LYS* 1.3 60.5 + - + +
101C PRO* 3.5 5.6 - - - -
102C ALA* 3.0 20.8 + - - +
122C ILE* 2.7 35.0 + - + +
123C ALA 4.3 0.2 - - - +
124C TYR* 3.7 16.2 - - + +
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Residues in contact with LYS 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 4.3 24.5 - - + -
29A ILE 4.7 8.0 + - - +
120A GLU* 2.9 29.0 + - - -
122A ILE* 5.3 8.7 - - - +
74B LYS* 6.0 1.0 - - - +
72C VAL* 3.9 0.2 - - - +
73C ILE* 1.3 84.9 - - + +
75C VAL* 1.3 67.9 + - - +
76C THR* 3.7 17.1 + - - +
101C PRO* 3.6 0.8 - - - +
102C ALA* 3.4 25.6 - - + +
104C VAL* 3.6 18.2 - - + -
121C ALA* 3.4 4.9 - - - +
122C ILE* 3.1 54.9 + - + +
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Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 5.1 5.8 - - + +
72C VAL* 3.5 22.7 - - + -
74C LYS* 1.3 82.4 - - - +
76C THR* 1.3 67.2 + - - +
77C VAL* 3.7 23.1 - - + -
92C TYR* 6.0 0.7 - - + -
96C PHE* 3.8 27.8 - - + -
101C PRO* 4.0 10.1 - - + -
102C ALA 2.9 10.8 + - - +
103C ARG* 3.6 9.2 - - + +
104C VAL* 3.0 25.3 + - - +
119C ILE* 3.8 17.3 - - + -
120C GLU 3.7 2.7 - - - +
121C ALA* 4.6 3.8 - - + -
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Residues in contact with THR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TYR* 4.4 5.8 - - - +
120A GLU* 4.9 2.0 + - - +
74C LYS* 3.7 23.1 + - - +
75C VAL* 1.3 77.7 + - - +
77C VAL* 1.3 62.9 + - - +
78C TYR* 3.4 34.2 - - + +
104C VAL* 3.4 21.8 - - + +
105C ALA* 6.0 0.2 - - - -
106C VAL* 6.0 1.1 - - + -
118C GLU 4.0 0.7 - - - +
119C ILE* 3.4 3.6 - - - +
120C GLU* 2.8 60.4 + - - +
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Residues in contact with VAL 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 5.7 0.7 - - - +
75C VAL* 3.7 21.1 - - + -
76C THR* 1.3 76.9 - - - +
78C TYR* 1.3 64.8 + - - +
79C LEU* 4.0 13.2 + - + +
92C TYR* 4.2 15.7 - - + +
103C ARG* 4.9 13.0 - - + +
104C VAL 2.9 14.5 + - - +
105C ALA* 3.4 10.5 - - + +
106C VAL* 3.2 26.3 + - - +
117C ILE* 3.8 20.4 - - + -
118C GLU 3.6 1.8 - - - +
119C ILE* 3.8 23.8 - - + -
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Residues in contact with TYR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TYR* 4.5 8.9 + + - -
76B THR* 4.4 3.0 - - + +
78B TYR* 4.4 18.2 + + - -
104B VAL* 3.9 15.7 - - + +
106B VAL* 3.7 32.8 - - + -
76C THR* 3.4 27.8 - - + +
77C VAL* 1.3 72.9 - - - +
79C LEU* 1.3 59.7 + - - +
106C VAL* 3.6 23.8 - - + +
108C VAL* 4.2 8.7 - - + -
111C LEU* 3.8 21.4 - - + +
117C ILE* 3.3 8.8 - - - +
118C GLU* 2.7 51.0 + - + +
120C GLU* 2.8 33.3 + - + -
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Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ILE* 4.4 16.8 - - + -
77C VAL* 4.2 13.2 - - + +
78C TYR* 1.3 81.1 - - - +
80C LYS* 1.3 55.4 + - - +
81C ASP 4.9 2.2 - - - +
92C TYR* 5.2 2.0 - - - +
105C ALA* 5.2 9.0 - - + -
106C VAL 3.0 15.2 + - - +
107C GLU* 3.1 19.3 - - + +
108C VAL* 2.7 37.6 + - - +
111C LEU* 4.7 1.8 - - - -
116C LEU 3.7 6.3 - - - +
117C ILE* 3.9 29.2 - - + +
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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