Contacts of the strand formed by residues 89 - 103 (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 ASN 89 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75X LEU* 3.4 17.9 + - - +
77X CYS* 3.5 4.3 - - - -
86X ILE* 4.1 11.1 + - - +
88X MET* 1.3 83.5 + - - +
90X SER* 1.3 61.6 + - - +
91X VAL* 3.7 11.0 - - + -
124X CYS* 3.2 5.5 - - - -
125X VAL* 2.7 53.9 + - + +
127X PRO* 3.8 23.0 - - + +
47Y ARG* 5.1 2.9 + - - -
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Residues in contact with SER 90 (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* 2.8 31.5 - - - -
51X PRO* 4.8 0.2 - - - +
72X CYS* 3.9 15.6 - - - +
74X ASN* 3.1 29.2 + - - +
75X LEU* 3.2 10.9 + - - +
76X GLY 2.7 19.9 + - - -
89X ASN* 1.3 70.4 - - - +
91X VAL* 1.3 64.5 + - - +
92X PRO* 4.7 0.5 - - - +
123X THR 3.6 6.7 - - - -
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Residues in contact with VAL 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72X CYS* 3.3 5.8 - - - -
89X ASN* 4.1 9.9 - - + -
90X SER* 1.3 78.6 - - - +
92X PRO* 1.3 71.6 - - + +
122X CYS* 2.8 22.7 - - - +
123X THR* 3.0 33.2 + - + +
125X VAL* 3.8 27.4 - - + -
41Y SER* 3.8 22.0 - - - +
44Y ILE* 4.0 15.7 - - + -
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Residues in contact with PRO 92 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72X CYS* 3.8 14.4 - - - +
90X SER 4.7 0.4 - - - +
91X VAL* 1.3 91.9 - - + +
93X ILE* 1.3 63.0 + - - +
94X GLN* 5.5 4.3 - - + -
119X THR* 3.6 24.2 - - + -
121X GLY 3.5 5.6 - - - +
39Y SER 5.8 4.3 - - - +
40Y MET* 3.9 16.6 - - + +
41Y SER* 5.6 1.2 + - - +
44Y ILE* 3.9 8.3 - - - +
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Residues in contact with ILE 93 (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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92X PRO* 1.3 76.2 - - - +
94X GLN* 1.3 63.0 + - - +
119X THR* 3.6 2.9 - - - -
120X VAL* 3.0 28.7 + - + +
121X GLY 2.7 16.0 + - - +
123X THR* 3.8 37.9 - - + +
40Y MET* 3.8 10.8 - - + -
44Y ILE* 4.0 7.2 - - + -
52Y TRP* 4.1 13.0 - - + -
93Y ILE* 3.8 27.6 - - + -
120Y VAL* 3.5 40.6 - - + +
121Y GLY* 4.6 1.1 - - - -
122Y CYS 4.2 8.1 - - - +
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Residues in contact with GLN 94 (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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92X PRO* 5.7 3.8 - - + -
93X ILE* 1.3 75.0 - - - +
95X GLN* 1.3 60.3 - - - +
117X LEU* 3.3 37.1 + - + +
118X VAL 3.3 12.3 - - - +
119X THR* 3.9 19.6 + - + +
38Y VAL* 3.6 28.8 - - + +
39Y SER* 3.4 28.5 + - - +
40Y MET* 3.1 21.8 - - + +
120Y VAL* 3.9 9.1 - - - +
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Residues in contact with GLN 95 (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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93X ILE 4.2 0.4 + - - -
94X GLN* 1.3 75.5 - - - +
96X GLU* 1.3 83.3 + - - +
97X THR* 3.7 4.5 + - - +
117X LEU* 3.4 5.0 - - - +
118X VAL* 2.8 34.2 + - + +
120X VAL* 3.9 14.4 - - + -
38Y VAL* 5.6 0.9 - - - -
67Y VAL* 6.2 0.2 - - - +
95Y GLN* 3.8 21.1 - - + -
97Y THR* 4.9 6.3 - - - +
118Y VAL* 3.6 35.1 - - - +
120Y VAL* 3.5 24.5 - - + +
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Residues in contact with GLU 96 (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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95X GLN* 1.3 93.6 + - - +
97X THR* 1.3 61.1 + - - +
98X LEU* 6.2 0.9 - - + -
115X LYS* 3.3 43.4 + - + -
117X LEU* 3.7 21.7 - - + +
36Y GLN 3.5 9.4 - - - +
37Y ARG* 4.3 18.5 + - - +
38Y VAL* 4.5 10.6 + - + +
64Y PRO* 5.9 3.6 - - - +
97Y THR* 4.5 1.4 + - - -
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Residues in contact with THR 97 (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* 5.7 1.6 - - + -
95X GLN* 3.7 5.4 + - - -
96X GLU* 1.3 76.2 - - - +
98X LEU* 1.3 76.6 + - - +
99X VAL* 5.2 4.0 - - + -
115X LYS* 3.4 8.1 - - - +
116X VAL* 2.9 68.0 + - + +
118X VAL* 3.7 15.9 - - + -
95Y GLN* 5.1 2.7 - - - +
96Y GLU 4.2 4.3 + - - -
97Y THR* 2.5 34.4 + - - -
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Residues in contact with LEU 98 (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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64X PRO* 5.2 0.7 - - - +
96X GLU* 6.2 0.9 - - + -
97X THR* 1.3 92.8 + - - +
99X VAL* 1.3 67.6 + - - +
113X LEU* 4.4 18.2 - - + -
114X GLU 3.3 9.9 - - - +
115X LYS* 4.2 16.8 - - + -
31Y ILE* 4.9 6.1 - - + -
63Y TYR* 3.7 43.7 - - + +
64Y PRO* 4.3 6.7 - - + -
97Y THR* 3.8 2.6 + - - -
98Y LEU* 3.3 44.4 + - + +
100Y VAL* 4.2 11.9 - - + -
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Residues in contact with VAL 99 (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* 3.4 32.5 - - + -
63X TYR 3.2 16.6 - - - +
64X PRO* 3.2 20.0 - - + -
67X VAL* 4.3 9.2 - - + -
97X THR* 5.3 4.0 - - + -
98X LEU* 1.3 76.7 - - - +
100X VAL* 1.3 62.3 + - - +
113X LEU* 3.4 3.9 - - - +
114X GLU* 2.6 50.3 + - + +
116X VAL* 3.8 23.8 - - + -
98Y LEU* 4.4 2.5 - - - -
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Residues in contact with VAL 100 (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* 5.8 0.4 - - + -
62X ARG* 3.2 5.5 - - - +
63X TYR* 2.8 51.3 + - + +
99X VAL* 1.3 79.1 - - - +
101X ARG* 1.3 64.9 + - - +
111X PHE* 3.8 30.5 - - + -
112X GLN 3.7 8.5 - - - +
113X LEU* 4.2 14.1 - - + +
10Y PHE* 3.8 3.1 - - + -
11Y PHE* 4.1 12.6 - - + -
27Y LEU* 6.0 0.2 - - + -
98Y LEU* 4.0 15.7 - - + -
113Y LEU* 3.7 27.4 - - + -
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Residues in contact with ARG 101 (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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59X ASP* 2.9 35.5 + - - -
61X ASN* 3.4 13.8 + - + +
62X ARG* 3.7 28.0 - - - +
99X VAL 4.1 0.6 + - - -
100X VAL* 1.3 75.2 - - - +
102X ARG* 1.3 68.2 + - - +
103X LYS* 3.8 7.3 + - + +
111X PHE* 3.3 6.4 - - - -
112X GLN* 2.8 42.9 + - + +
114X GLU* 2.5 34.8 + - + +
32Y ILE* 4.0 23.1 - - + -
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Residues in contact with ARG 102 (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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58B TRP* 3.8 28.5 - - - -
61X ASN* 2.7 39.5 + - - +
101X ARG* 1.3 74.9 - - - +
103X LYS* 1.3 64.8 + - - +
104X HIS 4.5 5.0 + - - +
105X GLN* 5.1 9.1 - - - +
106X GLY 5.3 3.0 + - - +
109X VAL* 3.8 28.0 - - + +
110X SER 3.7 2.0 - - - -
111X PHE* 3.3 19.3 - - + -
9Y THR 4.4 1.8 + - - -
10Y PHE* 2.8 62.3 + - + -
12Y GLN 3.7 20.8 + - - -
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Residues in contact with LYS 103 (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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101X ARG* 4.2 10.5 - - + +
102X ARG* 1.3 77.0 - - - +
104X HIS* 1.3 85.0 + - + +
109X VAL* 3.1 5.7 - - - +
110X SER* 2.8 45.0 + - - +
111X PHE 4.5 0.2 - - - -
112X GLN* 2.5 46.9 + - + +
28Y ASP* 2.9 33.2 + - - +
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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