Contacts of the strand formed by residues 69 - 78 (chain D) in PDB entry 3Q2P
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 LYS 69 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D TYR 5.9 0.6 + - - -
32D LEU* 4.9 7.3 - - - +
65D TYR* 3.3 7.7 - - - -
66D ALA 3.0 27.8 + - - +
67D SER* 3.0 39.6 + - - -
68D ASP* 1.3 83.3 - - - +
70D LEU* 1.3 60.1 + - - +
71D PHE* 3.4 22.9 - - + -
92D PRO* 4.3 24.5 - - + -
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Residues in contact with LEU 70 (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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38D ILE* 4.1 13.7 - - + -
63D TYR* 3.7 25.1 - - + -
64D VAL 3.5 30.7 - - - +
65D TYR* 3.7 22.8 - - + +
69D LYS* 1.3 74.5 - - - +
71D PHE* 1.3 61.1 + - - +
92D PRO* 3.1 10.3 - - - +
93D VAL* 2.8 52.3 + - + +
95D PRO* 3.5 34.5 - - + -
96D PRO* 4.1 4.0 - - + -
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Residues in contact with PHE 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D TYR* 3.9 31.2 - + + -
32D LEU* 4.0 21.3 - - + -
63D TYR* 3.3 5.2 - - - -
64D VAL* 2.7 42.5 + - + +
66D ALA* 3.6 19.7 - - + -
69D LYS* 3.4 38.1 - - + -
70D LEU* 1.3 74.2 - - - +
72D ARG* 1.3 60.3 + - - +
89D PHE* 3.4 39.7 - + + -
90D ASN 3.4 7.2 - - - +
91D GLY* 3.6 26.5 - - - -
92D PRO* 4.2 4.9 - - + -
93D VAL* 4.1 5.2 - - - -
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Residues in contact with ARG 72 (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 GLN* 5.5 4.9 - - - +
63C TYR* 3.1 11.6 + - - -
72C ARG* 6.1 3.4 - - - +
61D GLN* 2.7 47.4 + - - +
62D LEU 3.3 9.8 + - - +
63D TYR* 3.9 32.5 - - + +
71D PHE* 1.3 74.0 - - - +
73D ALA* 1.3 84.4 + - - +
74D ASP* 2.9 32.3 + - - +
88D ARG* 3.9 1.6 - - - +
89D PHE* 3.4 2.6 - - - -
90D ASN* 2.9 38.5 + - + +
93D VAL* 4.2 11.3 - - + +
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Residues in contact with ALA 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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19D ALA* 3.8 20.4 - - + -
60D TYR 3.4 1.0 - - - +
61D GLN* 3.4 1.0 - - - -
62D LEU* 2.8 39.8 + - + +
64D VAL* 4.4 8.5 - - + -
71D PHE 4.1 0.6 + - - -
72D ARG* 1.3 83.1 + - - +
74D ASP* 1.3 58.8 - - - +
75D ILE* 4.7 5.2 - - + -
86D LEU* 4.2 3.1 - - + -
88D ARG 3.3 5.2 - - - +
89D PHE* 3.7 25.8 - - + -
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Residues in contact with ASP 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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96C PRO* 5.2 1.6 - - - +
59D GLU* 2.6 39.0 - - - +
60D TYR 3.2 3.8 - - - -
61D GLN* 3.2 19.4 - - - +
72D ARG* 2.9 22.1 + - - +
73D ALA* 1.3 72.3 - - - +
75D ILE* 1.3 57.5 + - - +
86D LEU* 3.5 5.0 - - - +
87D LEU* 2.7 44.1 + - + +
88D ARG* 2.7 38.7 + - + -
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Residues in contact with ILE 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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15D LEU* 3.2 50.7 - - + +
18D PHE* 3.7 22.2 - - + -
19D ALA* 3.8 20.0 - - + -
59D GLU* 3.2 5.0 - - - +
60D TYR* 2.7 49.9 + - + +
62D LEU* 4.0 17.3 - - + -
73D ALA* 4.7 0.9 - - + -
74D ASP* 1.3 80.2 + - - +
76D SER* 1.3 72.8 + - - +
77D GLU* 5.5 0.2 - - + -
84D ARG* 4.6 2.7 - - - -
85D LYS 3.3 10.8 - - - +
86D LEU* 4.4 5.6 - - + -
87D LEU* 4.2 3.4 - - - -
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Residues in contact with SER 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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58D TYR 3.4 9.6 - - - -
59D GLU* 4.9 2.0 - - - -
75D ILE* 1.3 78.6 - - - +
77D GLU* 1.3 62.9 + - - +
83D GLY 3.6 0.4 - - - +
84D ARG* 3.1 4.9 - - - -
85D LYS* 2.9 52.3 + - - +
87D LEU* 3.6 23.7 - - - +
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Residues in contact with GLU 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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11D PHE* 4.2 8.2 - - - -
57D GLY* 3.4 0.9 - - - -
58D TYR* 2.8 52.7 + - + +
60D TYR* 4.1 26.6 + - + -
75D ILE* 5.5 0.2 - - + -
76D SER* 1.3 77.0 - - - +
78D ASP* 1.3 65.8 + - - +
82D ARG* 4.0 27.7 - - - +
83D GLY 2.9 9.0 - - - +
84D ARG* 2.7 42.6 + - + +
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Residues in contact with ASP 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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56D LYS* 3.2 15.9 - - - +
57D GLY* 4.2 3.1 - - - -
77D GLU* 1.3 75.4 - - - +
79D TYR* 1.3 56.6 + - - +
80D LYS* 3.0 34.7 + - - -
81D THR* 2.7 43.9 + - - +
82D ARG* 2.6 35.0 + - - -
83D GLY* 2.9 13.1 + - - +
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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