Contacts of the strand formed by residues 76 - 83 (chain D) in PDB entry 3PJV
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 TYR 76 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D HIS* 3.3 35.4 + + - -
45D ALA* 3.4 30.7 - - + +
70D ILE* 3.6 40.3 - - + +
71D PHE* 3.3 22.5 + - + -
73D SER* 3.9 3.4 - - - -
74D GLY* 3.2 7.0 - - - +
75D TYR* 1.3 94.7 - + + +
77D SER* 1.3 64.6 + - - +
78D SER 4.1 11.4 - - - +
79D ILE* 4.1 12.6 - - + -
95D GLY* 4.8 1.6 + - - -
133F VAL* 3.3 19.1 - - + -
134F VAL 3.3 7.4 - - - +
135F SER* 3.6 11.0 - - - -
136F HIS* 4.4 3.5 - - - -
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Residues in contact with SER 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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71D PHE* 4.3 0.2 - - - -
76D TYR* 1.3 72.3 - - - +
78D SER* 1.3 63.1 + - - +
94D ASN* 3.5 1.6 - - - +
95D GLY* 2.8 33.9 + - - +
96D ILE 5.0 0.7 - - - -
97D PRO* 3.9 23.4 - - - +
134F VAL* 2.8 24.2 + - - +
135F SER 4.0 2.4 + - - -
136F HIS* 3.4 37.1 - - - +
137F PRO* 4.3 2.9 - - - +
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Residues in contact with SER 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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71D PHE* 4.3 2.9 - - - -
76D TYR* 3.2 1.6 - - - -
77D SER* 1.3 83.3 - - - +
79D ILE* 1.3 71.0 + - - +
80D ARG* 6.2 0.9 - - - -
93D ARG 3.2 7.6 - - - -
94D ASN* 3.5 20.6 - - - -
132F GLU 4.4 0.7 + - - -
133F VAL* 3.5 0.2 - - - -
134F VAL* 3.0 51.8 + - - +
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Residues in contact with ILE 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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49D LEU* 3.6 26.0 - - + -
67D VAL* 3.9 20.0 - - + +
70D ILE* 4.0 26.5 - - + -
71D PHE* 4.0 32.5 - - + +
76D TYR* 4.1 15.0 - - + -
78D SER* 1.3 81.3 - - - +
80D ARG* 1.3 68.8 + - - +
81D VAL* 5.0 0.2 - - + -
92D GLU* 3.3 2.8 - - - +
93D ARG* 2.9 33.6 + - + +
131F VAL* 4.6 1.6 - - + -
132F GLU 3.2 10.1 - - - +
133F VAL* 4.2 13.9 - - + -
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Residues in contact with ARG 80 (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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78D SER* 6.2 1.1 - - - -
79D ILE* 1.3 75.3 - - - +
81D VAL* 1.3 66.2 + - - +
82D VAL* 3.3 28.0 - - + +
87D ASP* 4.6 6.3 + - - -
89D THR* 2.8 43.5 + - + +
91D VAL* 3.5 4.9 - - - -
92D GLU* 4.0 16.5 + - + +
130F ARG* 3.7 4.4 - - - +
131F VAL* 3.5 2.9 - - - +
132F GLU* 2.8 65.8 + - + +
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Residues in contact with VAL 81 (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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53D LEU* 4.0 22.9 - - + -
57D ILE* 4.9 3.8 - - + -
63D VAL* 5.1 2.0 - - + -
67D VAL* 3.9 16.4 - - + -
79D ILE* 5.0 2.5 - - + -
80D ARG* 1.3 78.3 - - - +
82D VAL* 1.3 62.1 + - - +
89D THR* 3.6 3.6 - - - +
90D ILE* 2.8 48.6 + - + -
91D VAL* 2.9 35.0 + - + +
129F ALA* 4.0 15.5 - - + -
130F ARG 3.4 5.2 - - - +
131F VAL* 4.4 12.8 - - + -
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Residues in contact with VAL 82 (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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80D ARG* 3.3 47.6 - - + +
81D VAL* 1.3 76.2 - - - +
83D ASP* 1.3 73.3 + - - +
84D LEU* 3.4 3.5 + - + +
87D ASP* 4.0 23.6 - - - +
88D GLN 3.6 9.9 - - - +
89D THR* 4.7 1.1 - - - +
90D ILE* 4.2 2.7 - - - -
129F ALA* 3.1 6.2 - - - -
130F ARG* 2.8 63.3 + - + +
132F GLU* 4.3 7.2 - - - +
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Residues in contact with ASP 83 (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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82D VAL* 1.3 71.2 - - - +
84D LEU* 1.3 54.4 + - - +
85D LYS* 2.8 25.4 + - - +
86D THR* 3.0 29.7 + - - +
87D ASP* 2.6 35.9 + - - -
88D GLN* 2.9 17.2 + - + +
90D ILE* 3.7 26.0 - - + +
123F ARG* 5.5 4.3 + - - -
128F ALA 3.8 8.9 - - - +
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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