Contacts of the strand formed by residues 110 - 125 (chain X) in PDB entry 1JPY
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 SER 110 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102X ARG* 3.7 0.2 - - - -
103X LYS* 2.8 33.6 + - - +
104X HIS* 3.3 21.5 + - - -
108X SER 3.8 1.6 + - - -
109X VAL* 1.3 74.8 - - - +
111X PHE* 1.3 71.9 + - - +
26Y LYS* 3.7 25.6 + - - -
28Y ASP* 2.9 33.6 + - - -
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Residues in contact with PHE 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X LEU* 4.4 11.9 - - + -
100X VAL* 3.8 10.8 - - + -
101X ARG 3.3 3.4 - - - -
102X ARG* 3.3 24.9 - - + -
103X LYS* 4.5 0.4 - - - -
109X VAL* 3.9 22.9 - - + -
110X SER* 1.3 83.9 - - - +
112X GLN* 1.3 62.5 + - - +
10Y PHE* 3.3 36.8 - + - -
11Y PHE* 3.6 46.2 - + - -
12Y GLN 5.4 0.2 - - - -
25Y MET* 4.0 19.1 - - + -
26Y LYS 3.0 16.0 + - - +
27Y LEU* 3.2 8.7 - - + +
28Y ASP* 3.0 26.4 + - - +
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Residues in contact with GLN 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X VAL* 4.2 1.5 - - - +
101X ARG* 2.8 38.4 + - + +
103X LYS* 2.5 42.5 + - + +
111X PHE* 1.3 76.7 - - - +
113X LEU* 1.3 69.9 + - - +
27Y LEU* 4.0 3.6 - - - -
28Y ASP* 4.0 14.4 - - + +
29Y ILE 3.5 12.6 + - - -
30Y GLY* 3.2 26.7 + - - +
32Y ILE* 3.7 31.0 - - + +
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Residues in contact with LEU 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X PHE* 4.2 19.5 - - + -
98X LEU* 4.4 21.8 - - + -
99X VAL 3.4 6.1 - - - +
100X VAL* 4.2 15.0 - - + -
112X GLN* 1.3 77.4 - - - +
114X GLU* 1.3 60.1 + - - +
27Y LEU* 4.4 19.2 - - + +
28Y ASP 5.3 0.2 + - - -
30Y GLY 4.0 3.6 + - - +
31Y ILE* 3.6 23.9 - - + -
32Y ILE* 3.1 23.5 + - - +
63Y TYR* 4.7 1.1 - - + -
100Y VAL* 3.5 27.4 - - + -
113Y LEU* 3.8 27.4 - - + -
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Residues in contact with GLU 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X ARG* 5.6 1.3 + - - -
98X LEU* 3.3 5.4 - - - -
99X VAL* 2.6 51.5 + - + +
101X ARG* 2.5 48.3 + - + +
112X GLN 4.8 1.3 - - - +
113X LEU* 1.3 77.1 - - - +
115X LYS* 1.3 75.2 + - - +
116X VAL* 4.2 8.6 - - + +
31Y ILE* 4.4 2.5 - - - -
32Y ILE* 3.7 33.2 - - + -
33Y ASN* 4.3 7.9 + - - +
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Residues in contact with LYS 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96X GLU* 3.3 39.2 + - + -
97X THR 3.4 11.2 - - - +
98X LEU* 4.2 9.4 - - + -
114X GLU* 1.3 79.5 - - - +
116X VAL* 1.3 69.9 + - - +
117X LEU* 4.8 2.2 - - + -
31Y ILE* 4.0 10.4 - - + +
32Y ILE 2.9 9.6 + - - +
33Y ASN* 3.3 37.8 + - - +
34Y GLU* 2.6 28.7 + - - +
36Y GLN* 3.3 29.2 + - + +
37Y ARG* 5.4 4.9 - - - +
63Y TYR* 5.4 5.8 - - - -
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Residues in contact with VAL 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X ARG* 5.8 3.1 - - - +
67X VAL* 4.4 12.8 - - + -
69X GLN* 4.5 4.3 - - - +
97X THR* 2.9 38.7 + - + +
99X VAL* 3.8 36.3 - - + -
114X GLU* 3.9 12.6 - - - +
115X LYS* 1.3 79.2 - - - +
117X LEU* 1.3 69.0 + - - +
118X VAL* 3.6 21.1 - - + -
36Y GLN* 4.6 3.6 - - - +
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Residues in contact with LEU 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X GLN* 3.0 20.3 + - - +
94X GLN* 3.3 29.3 + - - +
95X GLN 3.4 3.6 - - - +
96X GLU* 3.7 39.5 - - + +
115X LYS* 4.8 2.0 - - + -
116X VAL* 1.3 74.1 - - - +
118X VAL* 1.3 61.0 + - - +
119X THR* 5.1 0.2 + - - -
36Y GLN* 3.3 44.5 - - + +
37Y ARG 3.6 20.4 - - - +
38Y VAL* 4.3 10.1 - - + +
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Residues in contact with VAL 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67X VAL* 4.1 13.2 - - + -
68X VAL 3.2 26.7 - - - +
69X GLN* 3.6 4.9 - - - +
94X GLN* 3.3 5.0 - - - -
95X GLN 2.8 37.7 + - - +
97X THR* 3.7 17.7 - - + -
116X VAL* 3.6 20.2 - - + -
117X LEU* 1.3 79.0 - - - +
119X THR* 1.3 71.6 + - - +
120X VAL* 3.4 6.3 + - + +
95Y GLN* 4.2 30.7 - - + +
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Residues in contact with THR 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X VAL* 4.4 0.9 - - - +
69X GLN* 3.0 16.4 + - - -
70X ALA* 2.8 58.6 + - + +
71X GLN* 5.1 0.9 - - - -
92X PRO* 3.6 31.2 - - + -
93X ILE 3.6 7.4 - - - +
94X GLN* 3.9 16.1 + - + +
117X LEU 5.1 0.2 + - - -
118X VAL* 1.3 75.3 - - - +
120X VAL* 1.3 59.7 + - - +
121X GLY 4.4 4.3 - - - +
122X CYS* 5.6 0.4 - - - -
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Residues in contact with VAL 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X MET* 5.9 1.3 - - + +
52X TRP* 3.9 11.1 + - - -
54X TYR* 4.1 9.7 + - - -
70X ALA* 3.8 3.2 - - - +
93X ILE* 3.0 12.3 + - + +
95X GLN* 3.9 9.0 - - + +
118X VAL* 3.8 16.4 - - - +
119X THR* 1.3 74.8 - - - +
121X GLY* 1.3 57.6 + - - +
93Y ILE* 3.1 31.3 - - + +
94Y GLN 3.9 11.9 - - - +
95Y GLN* 3.8 39.7 - - + +
120Y VAL* 3.9 15.3 - - + -
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Residues in contact with GLY 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52X TRP* 3.7 21.1 - - - -
70X ALA* 3.9 8.7 - - - -
92X PRO* 3.5 3.3 - - - +
93X ILE* 2.7 36.3 + - - +
119X THR* 3.3 3.8 - - - +
120X VAL* 1.3 81.7 - - - +
122X CYS* 1.3 59.7 + - - -
93Y ILE* 4.6 6.0 - - - +
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Residues in contact with CYS 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X SER* 2.9 22.5 + - - +
52X TRP* 3.2 23.4 - - - -
71X GLN* 4.0 1.3 - - - -
72X CYS* 2.0 60.8 - - + -
91X VAL 2.8 14.8 - - - +
92X PRO* 4.0 2.7 - - - -
93X ILE* 4.3 4.9 - - - +
119X THR* 5.6 0.7 - - - -
121X GLY* 1.3 80.1 - - - -
123X THR* 1.3 50.9 + - - +
93Y ILE* 4.1 0.3 - - - +
123Y THR* 2.7 26.2 + - - -
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Residues in contact with THR 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X SER* 3.0 11.7 + - - -
91X VAL* 3.0 45.1 + - + -
93X ILE* 3.8 10.7 - - + +
122X CYS* 1.3 73.0 - - - +
124X CYS* 1.3 62.2 + - - +
125X VAL* 4.6 3.4 - - + -
44Y ILE* 3.8 23.8 - - + -
48Y SER* 2.7 28.0 + - - +
50Y SER* 3.8 1.7 + - - -
52Y TRP* 4.3 2.9 - - + -
122Y CYS 3.1 20.2 + - - -
123Y THR* 3.8 6.7 - - - +
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Residues in contact with CYS 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X THR* 3.3 23.3 + - - +
50X SER* 3.5 3.5 + - - -
77X CYS* 2.0 47.1 - - + -
88X MET* 3.8 12.8 - - - -
89X ASN 3.2 3.4 - - - -
123X THR* 1.3 79.3 + - - +
125X VAL* 1.3 63.9 + - - +
48Y SER* 3.2 3.8 - - - -
49Y THR* 2.8 48.2 + - - +
50Y SER* 5.2 0.6 + - - -
123Y THR* 4.9 1.2 + - - +
124Y CYS 5.4 0.4 - - - +
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Residues in contact with VAL 125 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88X MET* 3.3 15.1 - - - +
89X ASN* 2.7 48.9 + - + +
91X VAL* 3.8 26.7 - - + -
123X THR* 4.6 0.7 - - + -
124X CYS* 1.3 74.1 - - - +
126X THR* 1.3 62.6 + - - +
41Y SER* 5.2 0.2 - - - +
44Y ILE* 3.9 23.3 - - + +
47Y ARG* 3.1 50.7 - - + +
48Y SER* 3.5 10.3 - - - +
49Y THR 4.7 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