Contacts of the strand formed by residues 74 - 78 (chain D) in PDB entry 5DQZ
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 LEU 74 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C TYR* 3.6 1.6 - - - -
50D ALA 3.1 11.2 + - - +
51D CYS* 3.3 24.4 - - - -
52D ILE 2.8 26.9 + - - -
72D GLY 3.8 2.6 + - - -
73D THR* 1.3 71.9 - - - +
75D LEU* 1.3 64.1 + - - +
76D VAL* 3.7 14.8 - - + -
88D SER* 3.8 7.0 - - - +
89D GLY 3.3 27.8 - - - +
90D GLN* 3.4 26.2 - - + +
196D LEU* 3.6 30.1 - - + +
197D ALA* 4.2 4.3 - - - +
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Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C TYR* 3.0 29.3 + - + +
25D ILE* 6.3 2.5 - - + -
32D PHE* 5.6 1.6 - - + -
52D ILE* 3.5 39.7 - - + +
54D LEU* 4.7 7.9 - - + -
60D VAL* 4.5 8.1 - - + -
64D ALA 5.5 0.9 - - - +
65D VAL* 4.4 20.2 - - + +
68D ALA* 4.4 19.7 - - + -
73D THR* 4.7 1.3 - - + -
74D LEU* 1.3 75.5 - - - +
76D VAL* 1.3 62.7 + - - +
77D TRP* 3.8 33.5 - - + -
89D GLY 2.8 29.6 + - - -
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Residues in contact with VAL 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D CYS* 3.8 13.0 - - - -
52D ILE 2.9 9.3 + - - -
53D MET* 3.5 19.3 - - + -
54D LEU* 2.8 27.1 + - - +
74D LEU* 3.7 28.5 - - + -
75D LEU* 1.3 79.1 - - - +
77D TRP* 1.3 61.5 + - - +
78D VAL* 3.3 20.1 + - + +
85D VAL* 4.3 14.8 - - + -
87D ALA 3.6 13.5 - - - +
88D SER* 4.7 3.8 - - - +
193D ALA* 5.5 2.2 - - - -
196D LEU* 4.5 15.9 - - + -
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Residues in contact with TRP 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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61C SER 5.3 0.2 - - - -
62C HIS* 3.8 35.7 - + + +
65C VAL* 3.6 42.9 - - + +
66C ARG 5.5 0.9 - - - +
77C TRP* 4.1 23.6 - + - -
86C TYR* 4.9 1.8 - + - -
88C SER* 4.0 11.2 - - - -
54D LEU* 3.4 31.7 - - + +
58D THR* 5.2 0.2 + - - -
60D VAL* 3.9 18.2 - - + +
75D LEU* 3.8 39.7 - - + -
76D VAL* 1.3 71.4 - - - +
78D VAL* 1.3 56.4 + - - +
85D VAL* 4.0 0.3 - - - -
86D TYR* 2.9 35.7 + - + +
87D ALA* 2.9 36.0 + - + +
89D GLY* 3.9 10.3 - - - -
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Residues in contact with VAL 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C HIS* 2.8 25.8 + - - -
19D PHE* 4.5 0.9 - - + -
53D MET* 4.0 26.5 - - + -
54D LEU 2.9 27.6 + - - +
55D GLU* 4.1 6.1 - - + +
56D PRO* 3.3 5.2 - - - +
76D VAL* 3.6 26.7 - - + +
77D TRP* 1.3 77.4 - - - +
79D GLY* 1.3 75.8 + - - +
82D GLY* 4.1 13.7 - - - +
84D ARG 3.2 13.7 - - - +
85D VAL* 4.2 10.3 - - + -
86D TYR* 3.9 5.2 - - - -
193D ALA* 5.0 2.0 - - + -
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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