Contacts of the strand formed by residues 110 - 125 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LYS* 2.7 40.5 + - - +
104A HIS* 3.8 15.8 - - - -
108A SER 4.0 0.9 - - - -
109A VAL* 1.3 77.5 - - - +
111A PHE* 1.3 68.9 + - - +
26B LYS* 3.5 23.1 - - - -
28B ASP* 2.6 37.1 + - - -
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Residues in contact with PHE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.4 11.0 - - + -
100A VAL* 3.7 13.9 - - + -
101A ARG 3.5 3.1 - - - -
102A ARG* 3.7 17.3 - - + -
109A VAL* 3.9 22.4 - - + -
110A SER* 1.3 83.4 + - - +
112A GLN* 1.3 55.8 + - - +
10B PHE* 3.2 38.6 - + - -
11B PHE* 3.4 45.8 - + - -
25B MET* 3.9 25.1 - - + -
26B LYS 2.7 21.6 + - - +
27B LEU* 2.9 10.4 - - + +
28B ASP 2.5 33.6 + - - -
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Residues in contact with GLN 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 3.8 3.4 - - - -
101A ARG* 2.8 35.7 + - + +
103A LYS* 2.9 34.7 + - + +
111A PHE* 1.3 76.4 - - - +
113A LEU* 1.3 65.0 + - - +
27B LEU* 4.0 3.1 - - - -
28B ASP* 3.7 17.7 - - + +
29B ILE 3.1 21.7 + - - -
30B GLY* 3.1 25.7 + - - +
31B ILE 5.0 0.2 - - - -
32B ILE* 3.6 28.8 - - + +
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.7 28.3 - - + -
25A MET* 6.1 1.1 - - + -
98A LEU* 4.6 19.7 - - + -
99A VAL 3.8 4.3 - - - +
100A VAL* 4.7 14.6 - - + -
112A GLN* 1.3 78.5 - - - +
114A GLU* 1.3 59.9 + - - +
27B LEU* 4.4 18.7 - - + +
28B ASP 4.7 0.4 + - - +
30B GLY 3.7 3.4 + - - +
31B ILE* 3.4 21.4 - - + -
32B ILE* 2.9 25.5 + - - +
63B TYR* 5.0 0.7 - - + -
100B VAL* 3.5 34.8 - - + -
113B LEU* 4.3 14.1 - - + -
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 5.1 5.1 + - - -
98A LEU* 3.3 7.5 - - - -
99A VAL* 2.7 60.3 + - + +
101A ARG* 2.7 43.3 + - + +
112A GLN 4.7 2.0 - - - +
113A LEU* 1.3 75.7 - - - +
115A LYS* 1.3 61.2 + - - +
116A VAL* 4.2 11.1 - - - +
31B ILE* 4.6 0.2 - - - -
32B ILE* 3.6 29.6 - - + -
33B ASN* 3.4 21.4 + - - +
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU* 2.8 41.9 + - + -
97A THR 3.2 10.5 - - - +
98A LEU* 3.9 11.7 - - + -
114A GLU* 1.3 72.1 - - - +
116A VAL* 1.3 61.8 + - - +
117A LEU* 4.8 1.8 - - + -
31B ILE* 4.1 6.9 - - + +
32B ILE 3.1 8.2 + - - +
33B ASN* 2.8 41.2 + - - +
34B GLU* 3.4 24.8 + - - +
36B GLN* 2.7 46.1 + - + +
37B ARG* 3.5 7.9 - - - +
63B TYR* 5.8 3.1 - - - -
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 5.4 7.0 - - - +
67A VAL* 4.2 13.0 - - + -
69A GLN* 4.5 2.2 - - - +
97A THR* 2.8 47.1 + - + +
99A VAL* 3.5 38.6 - - + -
114A GLU* 4.2 10.1 - - - +
115A LYS* 1.3 78.9 - - - +
117A LEU* 1.3 63.3 + - - +
118A VAL* 3.4 24.9 - - + -
33B ASN* 6.0 0.2 - - - +
36B GLN* 4.6 2.2 - - - -
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLN* 2.9 18.0 + - - -
94A GLN* 3.4 32.0 + - - +
95A GLN 3.4 3.6 - - - +
96A GLU* 3.6 40.6 - - + +
115A LYS* 4.8 1.3 - - + -
116A VAL* 1.3 73.0 - - - +
118A VAL* 1.3 61.4 + - - +
119A THR 4.1 0.3 + - - -
36B GLN* 3.9 33.2 + - + +
37B ARG 3.4 25.6 - - - +
38B VAL* 4.2 11.9 - - + +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A VAL* 3.8 15.0 - - + -
68A VAL 3.5 25.1 - - - +
69A GLN* 3.4 5.2 - - - +
94A GLN* 3.3 2.5 - - - -
95A GLN 2.7 40.0 + - - +
97A THR* 3.5 15.9 - - + -
116A VAL* 3.4 26.5 - - + -
117A LEU* 1.3 74.3 - - - +
119A THR* 1.3 69.4 + - - +
120A VAL* 3.5 15.4 + - + +
95B GLN* 4.1 21.8 - - + +
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Residues in contact with THR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL 4.1 1.0 - - - +
69A GLN* 2.8 14.9 + - - +
70A ALA* 2.8 61.5 + - + +
71A GLN* 5.1 0.9 - - - -
92A PRO* 3.8 30.2 - - + +
93A ILE 3.4 7.4 - - - +
94A GLN* 3.4 22.5 + - - +
117A LEU 4.1 0.2 + - - -
118A VAL* 1.3 74.8 - - - +
120A VAL* 1.3 59.9 + - - +
121A GLY 4.3 4.5 - - - +
122A CYS* 5.6 0.7 - - - -
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Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A MET* 5.9 0.7 - - + -
52A TRP* 3.6 15.1 + - - -
54A TYR* 4.0 9.2 + - - -
68A VAL 5.6 0.4 - - - -
70A ALA* 3.7 4.4 - - - +
93A ILE* 3.0 10.5 + - + +
95A GLN* 4.0 13.5 - - + -
118A VAL* 3.6 21.5 - - + +
119A THR* 1.3 74.9 - - - +
121A GLY* 1.3 58.2 + - - +
93B ILE* 3.2 28.2 - - + +
94B GLN 4.3 4.3 - - - +
95B GLN* 3.7 44.0 - - + +
120B VAL* 4.5 7.6 - - + -
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Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TRP* 3.4 26.5 - - - -
70A ALA* 3.8 3.5 - - - +
92A PRO* 3.6 3.3 - - - +
93A ILE* 2.7 33.1 + - - +
119A THR* 3.6 2.4 - - - +
120A VAL* 1.3 80.1 - - - +
122A CYS* 1.3 60.2 + - - -
93B ILE* 4.2 8.6 - - - +
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Residues in contact with CYS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A SER* 3.4 22.8 + - - +
52A TRP* 3.1 26.1 - - - -
71A GLN* 4.3 1.3 - - - -
72A CYS* 2.0 62.1 - - + -
91A VAL 3.3 7.2 - - - +
92A PRO* 4.2 3.1 - - - -
93A ILE* 4.0 4.0 - - - -
119A THR* 5.6 0.9 - - - -
121A GLY* 1.3 80.5 - - - -
123A THR* 1.3 59.9 + - - +
93B ILE* 4.1 1.2 - - - +
123B THR* 3.0 21.7 + - - -
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Residues in contact with THR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A SER* 3.0 11.4 + - - -
89A ASN 3.7 0.2 - - - +
91A VAL* 3.1 36.3 + - + +
93A ILE* 3.9 9.3 - - - +
122A CYS* 1.3 71.9 - - - +
124A CYS* 1.3 60.3 + - - +
125A VAL* 3.9 15.5 - - + -
44B ILE* 4.0 13.2 - - + -
48B SER* 2.7 32.1 + - - +
50B SER* 3.4 2.8 + - - -
52B TRP* 4.2 2.2 - - + -
122B CYS 2.4 29.1 + - - -
123B THR* 3.8 4.4 - - - -
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Residues in contact with CYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR* 3.6 19.3 - - - +
50A SER* 3.2 4.6 + - - +
77A CYS* 2.0 47.6 - - - -
88A MET* 3.8 22.7 - - - -
89A ASN 3.3 3.4 - - - -
123A THR* 1.3 75.6 + - - +
125A VAL* 1.3 59.3 + - - +
48B SER* 3.1 3.5 + - - -
49B THR* 2.7 46.0 + - - +
123B THR* 4.9 1.0 + - - +
124B CYS* 5.6 1.4 - - + +
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A MET* 3.7 12.0 - - - +
89A ASN* 2.8 48.0 + - + +
91A VAL* 3.5 25.6 - - + -
123A THR* 3.9 11.4 - - + -
124A CYS* 1.3 74.9 - - - +
126A THR* 1.3 60.1 + - - +
41B SER* 4.8 0.2 - - - +
44B ILE* 3.8 21.1 - - + +
47B ARG* 3.3 32.8 - - + +
48B SER* 3.6 25.6 - - - +
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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