Contacts of the strand formed by residues 73 - 79 (chain D) in PDB entry 5DSV
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 73 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D ASN* 3.6 10.4 - - - +
69D VAL* 3.3 33.2 + - + -
70D ASP* 3.5 15.9 + - + +
71D ARG 3.4 0.8 - - - -
72D HIS* 1.3 112.4 - - + +
74D GLY* 1.3 70.6 + - - +
106D ILE* 4.9 2.2 - - + -
108D LEU* 3.7 33.0 - - + -
111D LEU* 4.1 17.0 - - + -
137D LEU* 4.3 6.7 - - + -
138D GLY 3.4 3.4 - - - +
139D SER* 4.2 0.2 - - - -
224D HIS* 4.0 4.3 - - - -
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Residues in contact with GLY 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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47D PHE* 3.8 6.6 - - - -
67D PHE 3.4 6.5 - - - -
69D VAL 5.0 0.2 - - - -
73D VAL* 1.3 77.9 - - - +
75D MET* 1.3 60.3 + - - -
136D MET 3.5 0.7 - - - +
137D LEU* 3.2 6.8 - - - -
138D GLY 2.9 34.8 + - - -
224D HIS* 3.4 27.3 - - - -
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Residues in contact with MET 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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47D PHE* 5.2 0.8 - - - -
65D ARG 3.8 0.5 - - - +
66D LEU* 3.3 7.3 - - - +
67D PHE* 2.9 39.7 + - + +
69D VAL* 3.7 30.7 - - + +
74D GLY* 1.3 74.5 - - - -
76D ALA* 1.3 63.7 + - - +
77D VAL* 3.7 25.6 - - + -
84D ALA* 3.9 9.9 - - - +
87D LEU* 4.3 6.1 - - + +
88D ALA* 3.8 33.9 - - + +
91D ALA* 4.9 2.7 - - - -
135D PHE* 3.7 26.9 - - + -
136D MET 3.2 5.2 - - - +
137D LEU* 3.8 16.2 - - + -
224D HIS* 4.6 0.7 + - - -
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Residues in contact with ALA 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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36D ALA* 5.5 4.5 - - + -
37D ILE 5.5 1.1 - - - +
47D PHE* 3.6 30.1 - - + -
48D GLY 6.1 0.2 - - - +
49D VAL* 5.2 2.7 - - + -
65D ARG 3.5 4.9 - - - -
66D LEU* 3.4 22.2 - - + -
75D MET* 1.3 74.8 - - - +
77D VAL* 1.3 59.7 + - - +
135D PHE* 3.1 2.3 - - - -
136D MET* 2.8 39.2 + - + -
165D ILE* 3.7 7.5 - - - +
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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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36D ALA* 4.2 5.8 - - - +
65D ARG* 3.1 46.4 + - + +
67D PHE* 3.8 26.2 - - + -
75D MET* 3.7 34.1 - - + -
76D ALA* 1.3 78.8 - - - +
78D ALA* 1.3 63.3 + - - +
81D LEU* 4.1 17.3 - - + -
84D ALA* 3.9 15.3 - - + -
134D SER 3.6 5.6 - - - +
135D PHE* 3.7 4.3 - - + -
165D ILE* 4.1 1.8 - - - -
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Residues in contact with ALA 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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30D VAL* 3.8 14.0 - - + +
33D SER* 4.4 0.2 - - - +
34D SER 4.3 3.4 - - - +
36D ALA* 4.8 0.9 - - + -
65D ARG* 3.6 15.0 - - - +
77D VAL* 1.3 79.3 - - - +
79D GLY* 1.3 62.4 + - - +
133D CYS* 3.4 6.3 - - - +
134D SER 3.0 33.1 + - - +
165D ILE* 3.5 36.3 - - + +
166D GLY* 4.6 1.1 - - - +
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Residues in contact with GLY 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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29D ALA 3.6 14.4 - - - -
30D VAL* 3.7 7.8 - - - +
33D SER* 3.1 36.2 + - - -
65D ARG* 5.8 0.5 - - - -
78D ALA* 1.3 73.8 - - - +
80D LEU* 1.3 63.9 + - - -
81D LEU* 3.2 9.4 + - - +
132D GLY 3.8 1.3 - - - -
133D CYS* 4.6 0.2 - - - -
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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