Contacts of the strand formed by residues 89 - 103 (chain Y) 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 ASN 89 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47X ARG* 5.6 2.9 + - - +
75Y LEU* 2.9 33.3 + - - +
76Y GLY* 4.6 0.2 - - - -
77Y CYS* 3.7 5.6 - - - -
86Y ILE* 5.0 7.3 + - - +
87Y SER 5.4 1.4 - - - +
88Y MET* 1.3 79.8 + - - +
90Y SER* 1.3 61.0 + - - +
91Y VAL* 3.6 8.2 + - + -
124Y CYS* 3.3 4.9 - - - -
125Y VAL* 2.8 54.3 + - + +
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Residues in contact with SER 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Y SER* 3.0 33.2 - - - -
51Y PRO* 4.6 1.9 + - - +
72Y CYS* 4.1 17.5 - - - +
74Y ASN 2.9 30.3 + - - +
75Y LEU* 2.9 13.2 + - - +
76Y GLY 3.5 11.8 + - - -
77Y CYS* 4.6 0.2 - - - -
89Y ASN* 1.3 71.6 - - - +
91Y VAL* 1.3 64.8 + - - +
92Y PRO* 4.4 1.2 - - - +
123Y THR 3.7 4.3 - - - -
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Residues in contact with VAL 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41X SER* 3.7 19.7 - - - +
44X ILE* 3.2 29.4 - - + -
72Y CYS* 3.6 4.2 - - - -
89Y ASN* 3.6 7.6 + - + -
90Y SER* 1.3 80.0 - - - +
92Y PRO* 1.3 70.6 - - + +
122Y CYS* 3.2 1.9 - - - -
123Y THR* 3.0 35.1 + - + +
125Y VAL* 3.7 34.5 - - + -
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Residues in contact with PRO 92 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X SER 5.8 3.4 - - - +
40X MET* 3.8 17.0 - - + +
44X ILE* 3.8 8.5 - - - +
72Y CYS* 3.5 17.7 - - - +
90Y SER 4.4 0.9 - - - +
91Y VAL* 1.3 92.4 - - + +
93Y ILE* 1.3 61.0 + - - +
94Y GLN* 4.0 4.3 - - + -
119Y THR* 4.2 25.8 - - + +
121Y GLY 3.5 6.1 - - - +
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Residues in contact with ILE 93 (chain Y).
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* 3.7 10.3 - - + -
44X ILE* 4.3 14.1 - - + -
52X TRP* 3.9 16.4 - - + -
93X ILE* 3.8 27.1 - - + -
120X VAL* 3.1 40.8 - - + +
121X GLY 4.6 1.1 - - - -
122X CYS 4.1 7.4 - - - +
92Y PRO* 1.3 77.8 - - - +
94Y GLN* 1.3 60.9 + - - +
119Y THR* 3.5 3.9 - - - -
120Y VAL* 3.0 29.6 + - + +
121Y GLY 2.6 16.8 + - - +
122Y CYS 4.4 0.2 - - - -
123Y THR* 3.7 28.5 - - - +
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Residues in contact with GLN 94 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X VAL* 3.2 30.1 - - + +
39X SER* 3.1 33.9 + - - +
40X MET* 3.2 17.6 - - + +
120X VAL* 3.9 9.9 - - - +
92Y PRO* 5.5 4.9 - - + +
93Y ILE* 1.3 72.3 - - - +
95Y GLN* 1.3 62.8 + - - +
96Y GLU 4.3 0.2 + - - -
117Y LEU* 3.5 38.2 + - + +
118Y VAL 3.6 3.4 - - - +
119Y THR* 3.7 21.5 + - - +
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Residues in contact with GLN 95 (chain Y).
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* 6.1 1.4 - - - +
95X GLN* 3.8 24.0 - - + -
97X THR* 5.0 4.4 + - - +
118X VAL* 4.2 27.0 - - + +
120X VAL* 3.8 23.1 - - + +
94Y GLN* 1.3 76.6 - - - +
96Y GLU* 1.3 83.9 + - - +
97Y THR* 3.7 2.7 + - - +
117Y LEU* 4.5 2.9 - - - -
118Y VAL* 2.7 42.1 + - + +
120Y VAL* 3.5 23.7 - - + +
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Residues in contact with GLU 96 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36X GLN 3.8 4.5 - - - +
37X ARG* 4.6 6.9 - - - +
38X VAL* 5.0 10.2 + - + +
64X PRO* 4.9 14.2 - - - +
97X THR* 4.2 1.7 + - - -
94Y GLN 4.2 0.8 + - - -
95Y GLN* 1.3 96.0 + - - +
97Y THR* 1.3 63.6 + - - +
115Y LYS* 3.0 48.8 + - + +
117Y LEU* 3.3 21.5 - - + +
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Residues in contact with THR 97 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95X GLN* 4.9 7.4 - - - +
96X GLU 4.5 1.4 + - - -
97X THR* 2.5 30.8 + - - -
95Y GLN* 4.7 4.0 - - - -
96Y GLU* 1.3 77.1 - - - +
98Y LEU* 1.3 77.9 + - - +
99Y VAL* 4.7 4.9 - - + -
115Y LYS* 3.3 10.8 - - - +
116Y VAL* 2.8 53.9 + - + +
118Y VAL* 3.6 25.4 - - + -
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Residues in contact with LEU 98 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X ILE* 4.4 11.9 - - + -
63X TYR* 3.8 38.1 - - + +
64X PRO* 4.7 4.9 - - + -
97X THR* 3.9 2.4 + - - -
98X LEU* 3.3 46.1 + - + +
99X VAL* 4.4 0.4 - - - -
100X VAL* 4.0 17.5 - - + -
113X LEU* 6.6 0.2 - - + -
64Y PRO* 4.7 1.7 - - - +
97Y THR* 1.3 90.1 + - - +
99Y VAL* 1.3 67.2 + - - +
113Y LEU* 4.8 15.5 - - + -
114Y GLU 3.6 12.6 - - - +
115Y LYS* 3.9 18.4 - - + +
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Residues in contact with VAL 99 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X LEU* 4.6 0.7 - - - -
62Y ARG* 3.9 27.8 - - + -
63Y TYR 3.3 11.0 - - - +
64Y PRO* 4.1 13.7 - - + -
67Y VAL* 4.5 9.2 - - + -
97Y THR* 4.7 7.4 - - + -
98Y LEU* 1.3 80.8 - - - +
100Y VAL* 1.3 63.2 + - - +
113Y LEU* 3.6 4.0 - - - +
114Y GLU* 2.6 64.3 + - + +
116Y VAL* 3.6 26.5 - - + -
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Residues in contact with VAL 100 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X PHE* 3.6 2.6 - - + -
11X PHE* 4.2 7.9 - - + -
27X LEU* 5.6 0.7 - - + -
98X LEU* 4.2 4.9 - - + -
113X LEU* 3.5 31.4 - - + -
27Y LEU* 5.4 3.1 - - + -
62Y ARG* 3.2 5.7 - - - +
63Y TYR* 2.7 61.1 + - + +
99Y VAL* 1.3 76.3 - - - +
101Y ARG* 1.3 63.1 + - - +
111Y PHE* 4.0 35.9 - - + -
112Y GLN 3.8 8.1 - - - +
113Y LEU* 4.5 13.7 - - + +
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Residues in contact with ARG 101 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X PHE* 4.3 1.1 - - - -
32X ILE* 4.4 18.2 - - + -
59Y ASP* 3.0 31.1 + - - +
61Y ASN* 3.5 22.5 + - - +
62Y ARG* 3.5 28.1 - - - +
99Y VAL 3.8 1.0 + - - -
100Y VAL* 1.3 73.9 - - - +
102Y ARG* 1.3 72.1 + - - +
103Y LYS* 3.8 10.0 + - + +
111Y PHE* 3.4 5.2 - - - -
112Y GLN* 2.7 46.4 + - + +
114Y GLU* 2.8 36.1 + - + +
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Residues in contact with ARG 102 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X THR 5.0 3.2 + - - -
10X PHE* 3.2 51.3 + - + +
12X GLN 3.7 19.8 + - - -
13X LYS* 5.4 0.4 - - - +
60Y PRO 5.4 0.7 - - - -
61Y ASN* 2.9 43.0 + - - +
101Y ARG* 1.3 77.9 - - - +
103Y LYS* 1.3 66.4 - - - +
104Y HIS 4.1 14.1 + - - +
105Y GLN* 4.8 5.3 - - - +
106Y GLY* 5.1 7.3 + - - +
109Y VAL* 3.5 28.4 - - + +
110Y SER 3.8 2.7 - - - -
111Y PHE* 3.8 13.5 - - + -
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Residues in contact with LYS 103 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X ASP* 2.6 36.0 + - - +
101Y ARG* 4.3 11.7 - - + +
102Y ARG* 1.3 79.6 - - - +
104Y HIS* 1.3 93.0 + - + +
109Y VAL* 3.6 6.1 - - - +
110Y SER* 2.8 31.3 + - - +
112Y GLN* 3.3 41.1 + - + +
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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