Contacts of the strand formed by residues 90 - 101 (chain r) in PDB entry 4PJO
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 90 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75r THR* 3.3 4.8 + - - -
76r GLU* 2.8 60.3 + - + +
77r VAL* 4.9 5.4 - - + -
88r LYS 3.4 5.7 + - - +
89r PRO* 1.3 72.3 - - - +
91r ASN* 1.3 76.1 - - - +
92r LYS* 4.5 13.2 - - + +
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Residues in contact with ASN 91 (chain r).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44n TYR* 5.1 8.6 + - + -
46n ARG* 5.6 6.2 - - - +
74r TRP 3.8 6.7 - - - +
75r THR* 3.8 11.3 + - - -
89r PRO 4.2 2.9 + - - +
90r VAL* 1.3 85.3 - - - +
92r LYS* 1.3 67.9 + - - +
93r ASP* 5.8 1.6 - - - +
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Residues in contact with LYS 92 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1384 G 5.3 2.6 + - - -
1394 G 5.1 6.5 - - - +
73r MET* 3.3 3.6 - - - +
74r TRP* 3.0 63.0 + - + +
76r GLU* 3.6 45.1 + - + +
90r VAL* 4.5 15.0 - - + +
91r ASN* 1.3 83.5 - - - +
93r ASP* 1.3 68.2 + - - +
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Residues in contact with ASP 93 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46n ARG* 5.3 1.7 + - - -
71r LYS* 4.0 31.9 + - + +
72r GLU 3.1 12.6 - - - +
73r MET* 4.2 4.3 - - + -
74r TRP* 3.8 6.6 - - - -
91r ASN* 5.8 1.2 - - - +
92r LYS* 1.3 80.3 - - - +
94r ARG* 1.3 69.2 + - - +
95r TYR* 4.7 12.6 + - - -
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Residues in contact with ARG 94 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1364 G 5.7 0.2 - - - +
18q GLU* 2.4 32.7 + - - -
24q GLN* 4.8 8.7 + - - +
67q TYR* 3.1 19.6 + - - -
69q ILE* 3.9 10.3 - - - +
50r LYS* 5.5 2.5 - - - +
71r LYS* 3.4 3.1 - - - -
72r GLU* 2.6 53.3 + - - +
74r TRP* 4.1 11.6 - - + -
93r ASP* 1.3 80.8 - - - +
95r TYR* 1.3 67.1 + - - +
96r ILE* 3.6 26.4 + - + +
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Residues in contact with TYR 95 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69r ASN 6.0 0.9 - - - -
70r VAL 3.4 10.8 - - - +
71r LYS* 3.9 39.2 + - + -
93r ASP* 4.7 10.6 + - - -
94r ARG* 1.3 78.2 - - - +
96r ILE* 1.3 64.4 + - - +
97r SER 4.3 0.4 - - - -
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Residues in contact with ILE 96 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67q TYR* 4.5 5.4 - - + +
69q ILE* 4.0 34.1 - - + -
69r ASN* 3.7 0.7 - - - -
70r VAL* 2.8 39.5 + - + +
72r GLU* 4.2 12.8 - - + +
94r ARG* 3.6 45.3 - - + +
95r TYR* 1.3 79.4 - - - +
97r SER* 1.3 64.4 + - - +
98r LYS 4.2 3.1 - - - +
99r MET* 4.0 34.8 - - + -
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Residues in contact with SER 97 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69q ILE* 5.8 0.4 - - - +
72q ASP* 3.1 39.1 + - - -
68r GLU* 3.2 6.6 - - - +
69r ASN* 2.9 34.5 + - - +
70r VAL* 5.5 0.4 - - - -
95r TYR* 4.3 0.4 - - - -
96r ILE* 1.3 76.0 - - - +
98r LYS* 1.3 72.2 + - - +
99r MET 4.4 0.2 - - - -
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Residues in contact with LYS 98 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69q ILE* 3.7 4.3 - - - +
70q LEU* 2.7 47.9 + - + +
71q PRO 3.7 8.7 - - - +
72q ASP* 2.7 28.9 + - - +
73q SER* 3.6 3.6 + - - +
74q LEU* 2.8 31.8 + - + +
75q PRO* 5.1 0.2 - - - +
76q LEU* 3.8 27.2 - - + +
66r VAL* 6.2 0.2 - - + -
67r LEU 3.4 5.6 - - - +
68r GLU* 4.0 17.7 - - + -
96r ILE* 4.2 1.1 - - - +
97r SER* 1.3 91.4 + - - +
99r MET* 1.3 63.2 + - - +
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Residues in contact with MET 99 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67q TYR* 3.7 29.6 - - + -
68q PHE 3.2 14.6 - - - +
69q ILE* 4.5 2.0 - - + -
70q LEU* 4.0 6.1 - - - +
52r LEU* 3.5 28.0 - - + -
66r VAL* 3.3 9.2 - - - +
67r LEU* 2.8 49.0 + - + +
70r VAL* 3.9 31.0 - - + -
96r ILE* 4.0 25.6 - - + -
98r LYS* 1.3 76.2 - - - +
100r PHE* 1.3 60.1 + - - +
101r LEU* 4.0 15.5 - - + -
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Residues in contact with PHE 100 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3q LEU* 3.7 37.9 - - + -
6q PHE* 4.2 3.1 - + - -
7q LEU* 3.7 40.2 - - + -
36q MET* 3.8 16.8 - - + -
65q ILE* 6.1 0.2 - - + -
67q TYR* 3.1 6.5 - - - +
68q PHE* 2.8 47.6 + + + -
70q LEU* 4.1 6.9 - - + +
64r ASN* 3.7 26.9 - - + -
65r MET 3.4 5.4 - - - -
66r VAL* 3.8 17.5 - - + +
99r MET* 1.3 76.0 - - - +
101r LEU* 1.3 73.2 + - - +
102r ARG 4.1 2.5 - - - -
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Residues in contact with LEU 101 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66q ARG* 3.3 13.5 - - - +
67q TYR* 4.0 16.6 - - + -
44r ILE* 4.3 9.6 - - + -
46r CYS* 4.3 11.2 - - - -
52r LEU* 3.8 20.9 - - + -
63r CYS 5.2 0.2 - - - +
64r ASN* 3.4 3.6 - - - -
65r MET* 2.8 57.7 + - + +
67r LEU* 4.5 6.1 - - + -
99r MET* 4.0 12.0 - - + +
100r PHE* 1.3 76.7 - - - +
102r ARG* 1.3 82.4 + - - +
105r SER* 4.3 11.7 - - - -
106r VAL* 4.1 12.3 - - + -
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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