Contacts of the strand formed by residues 72 - 79 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D ILE* 6.0 0.2 - - + -
62D LEU* 3.8 33.7 - - + -
68D SER 4.2 0.7 - - - +
69D LEU 3.5 11.4 - - - +
70D ASN 3.3 1.0 - - - -
71D ASP* 1.3 77.7 - - - +
73D ILE* 1.3 62.5 + - - +
74D LYS 4.1 1.1 - - - +
75D VAL* 3.5 32.1 - - + -
96D PHE* 3.6 22.9 - - + -
99D SER* 4.3 7.1 + - - +
101D PRO* 3.5 22.5 - - + +
121D ALA* 4.4 8.5 - - + -
122D ILE 3.6 11.2 - - - +
123D ALA* 4.0 3.1 - - + +
2E LYS* 4.3 8.1 + - - -
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Residues in contact with ILE 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D PHE* 4.0 7.6 - - + -
71D ASP 3.8 10.1 - - - +
72D VAL* 1.3 77.7 - - - +
74D LYS* 1.3 65.8 + - + +
101D PRO* 3.6 6.1 - - - -
102D ALA* 2.7 23.4 + - - +
122D ILE* 2.9 33.4 + - + +
123D ALA* 4.4 0.4 - - - -
124D TYR* 4.0 13.2 - - + -
2E LYS* 3.9 14.1 - - + -
21E ILE* 3.1 39.6 - - + +
23E ALA* 3.8 12.6 - - + -
28E PHE* 3.7 32.9 - - + +
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Residues in contact with LYS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D VAL 3.8 0.4 - - - -
73D ILE* 1.3 84.2 - - + +
75D VAL* 1.3 70.8 + - - +
76D THR* 4.0 15.9 - - - +
101D PRO* 3.9 0.2 - - - +
102D ALA* 3.2 14.8 - - + +
103D ARG* 5.6 0.4 - - - -
104D VAL* 5.2 4.3 - - + -
121D ALA* 3.2 3.3 - - - -
122D ILE* 2.8 52.4 + - + +
28E PHE* 3.7 32.8 - - + -
29E ILE 5.7 4.7 - - - +
74E LYS* 5.2 6.5 - - - +
76E THR* 5.5 0.6 + - - -
120E GLU* 2.8 31.4 + - - -
122E ILE* 4.1 23.8 - - + +
74F LYS* 5.4 5.0 - - - +
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Residues in contact with VAL 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D VAL* 3.5 22.9 - - + -
74D LYS* 1.3 82.2 - - - +
76D THR* 1.3 68.9 + - - +
77D VAL* 4.1 10.5 - - + -
92D TYR* 3.6 30.1 - - + +
96D PHE* 4.2 9.4 - - + -
101D PRO* 4.1 6.7 - - + -
102D ALA 2.9 8.1 + - - +
103D ARG* 3.3 6.8 - - + +
104D VAL* 3.1 22.7 + - - +
119D ILE* 3.5 22.9 - - + -
120D GLU 3.4 11.4 - - - +
121D ALA* 4.0 7.0 - - + +
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Residues in contact with THR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D LYS* 4.0 19.4 - - - +
75D VAL* 1.3 76.9 + - - +
77D VAL* 1.3 66.0 + - - +
78D TYR* 3.5 35.0 - - + +
104D VAL* 3.4 26.7 - - + +
118D GLU 3.9 0.7 - - - +
119D ILE* 3.4 5.2 - - - +
120D GLU* 2.9 55.1 + - - +
78E TYR* 4.4 4.3 - - - +
120E GLU* 4.8 2.9 + - - +
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Residues in contact with VAL 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D VAL* 4.1 12.3 - - + -
76D THR* 1.3 78.1 - - - +
78D TYR* 1.3 62.9 + - - +
79D LEU* 4.0 10.5 - - + -
88D MET* 4.0 19.3 - - + -
92D TYR* 4.4 6.5 - - + -
103D ARG* 4.2 18.8 - - - -
104D VAL 2.9 10.0 + - - +
105D ALA* 3.6 7.0 - - + -
106D VAL* 3.1 29.5 + - - +
117D ILE* 3.8 31.2 - - + -
118D GLU 3.7 2.5 - - - -
119D ILE* 3.9 18.6 - - + -
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Residues in contact with TYR 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D THR* 3.5 24.7 - - + +
77D VAL* 1.3 73.6 - - - +
79D LEU* 1.3 62.6 + - - +
106D VAL* 3.6 23.8 - - + -
108D VAL* 3.8 15.5 - - + -
111D LEU* 3.5 22.8 - - + +
117D ILE* 3.3 7.4 - - - +
118D GLU* 2.8 47.6 + - + +
119D ILE* 5.1 0.2 - - - -
120D GLU* 2.9 28.5 + - + -
78E TYR* 4.5 10.8 + + - -
76F THR* 4.4 8.0 - - - +
78F TYR* 4.6 7.4 + + - -
104F VAL* 3.6 26.3 - - + +
106F VAL* 3.7 24.9 - - + -
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Residues in contact with LEU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ILE* 4.4 11.9 - - + -
77D VAL* 4.1 8.7 - - + -
78D TYR* 1.3 75.6 - - - +
80D LYS* 1.3 60.5 + - - +
81D ASP 4.0 21.5 - - - +
82D MET* 5.0 2.9 - - - +
84D ASP 4.3 1.3 - - - +
85D PHE* 3.8 35.9 - - + +
88D MET* 4.5 10.8 - - + -
105D ALA* 6.1 4.3 - - + -
106D VAL 2.9 14.4 + - - +
107D GLU* 3.4 5.7 - - + -
108D VAL* 2.9 31.2 + - - +
111D LEU* 4.2 0.9 - - - -
116D LEU 3.6 4.5 - - - +
117D ILE* 3.4 41.5 - - + -
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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