Contacts of the strand formed by residues 87 - 94 (chain A) in PDB entry 4JNX
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 GLY 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLY 3.8 0.5 - - - +
43A PHE* 3.6 1.9 - - - -
44A GLY* 2.8 37.0 + - - +
86A ILE* 1.3 73.8 - - - +
88A CYS* 1.3 59.7 + - - -
89A THR* 5.1 1.3 - - - -
103A GLY 3.6 6.3 - - - -
409B U 5.7 1.3 - - - +
412G U 3.9 14.6 - - - -
413G G 3.3 26.9 + - - -
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Residues in contact with CYS 88 (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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41A TRP* 5.2 0.9 - - + -
42A GLY 3.1 7.4 - - - +
43A PHE* 3.9 20.2 - - + -
81A PHE* 4.5 5.8 - - - -
86A ILE* 4.0 6.7 - - - -
87A GLY* 1.3 79.6 - - - -
89A THR* 1.3 61.7 + - - +
102A SER* 3.2 6.2 - - - -
103A GLY 2.9 30.0 + - - +
105A SER* 3.9 32.5 - - - -
108A LEU* 4.4 14.8 - - + -
111A LEU* 3.6 22.9 - - + +
412G U 4.1 0.4 + - - -
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Residues in contact with THR 89 (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 SER* 3.9 1.2 + - - +
41A TRP* 3.4 10.5 - - - -
42A GLY* 2.7 41.7 + - - -
87A GLY 5.1 0.7 - - - -
88A CYS* 1.3 77.7 + - - +
90A TYR* 1.3 62.1 - - - +
91A SER* 4.3 3.0 + - - +
100A THR* 3.1 36.3 - - + -
101A VAL 3.2 5.8 - - - +
102A SER* 3.5 10.2 - - - -
409B U 4.8 10.2 + - - -
410B G 4.3 16.8 - - - +
412G U 4.8 7.4 + - - -
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Residues in contact with TYR 90 (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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39A GLU* 2.4 40.9 + - + +
40A SER 3.2 13.9 - - - -
41A TRP* 3.5 39.8 - + + -
68A TRP* 3.5 15.5 - + - -
89A THR* 1.3 75.0 - - - +
91A SER* 1.3 74.4 + - - +
92A ILE* 3.6 28.4 - - + +
99A ILE 5.3 1.1 - - - -
100A THR* 3.2 4.2 - - - +
101A VAL* 2.8 44.1 + - + +
115A ALA* 3.6 36.1 - - + -
118A SER* 5.5 1.1 - - - -
119A LYS* 3.5 14.6 - - + +
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Residues in contact with SER 91 (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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39A GLU* 3.1 5.9 - - - +
40A SER* 2.8 51.8 + - - +
89A THR* 4.7 3.8 - - - -
90A TYR* 1.3 81.6 - - - +
92A ILE* 1.3 62.6 + - - +
98A SER* 6.3 1.3 - - - -
99A ILE 3.3 10.1 - - - -
100A THR* 3.6 17.7 - - - -
410B G 5.0 1.2 + - - -
411B C 4.5 12.5 - - - -
501B MG 3.7 13.9 - - - -
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Residues in contact with ILE 92 (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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37A PHE* 3.8 21.8 - - + -
38A LYS 3.3 12.6 - - - +
39A GLU* 4.4 0.2 - - + -
90A TYR* 3.6 32.3 - - + +
91A SER* 1.3 77.5 - - - +
93A ARG* 1.3 65.2 + - - +
94A PHE 4.4 0.2 - - - -
97A VAL 3.9 0.5 - - - +
98A SER* 3.3 3.9 - - - -
99A ILE* 2.9 47.3 + - + +
118A SER* 5.1 0.2 - - - -
119A LYS* 3.8 33.0 - - + +
122A LEU* 3.9 23.7 - - + +
123A LEU* 4.3 10.1 - - + -
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Residues in contact with ARG 93 (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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37A PHE* 3.6 4.5 - - - +
38A LYS* 2.9 55.2 + - + +
92A ILE* 1.3 76.2 - - - +
94A PHE* 1.3 67.7 + - - +
96A GLY* 3.3 38.5 + - - +
97A VAL 3.2 6.5 - - - +
98A SER* 2.9 23.3 + - - +
122A LEU* 4.4 0.4 - - - -
412B U 3.3 30.3 + - - +
413B G 2.8 32.1 + - - -
102D SER 4.2 0.6 + - - -
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Residues in contact with PHE 94 (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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34A PRO* 3.7 23.3 - - + -
36A GLY* 3.7 21.5 - - - -
37A PHE* 3.7 12.3 - - + -
54A TYR* 3.6 38.8 - + - -
56A ARG* 4.2 13.5 - - + -
92A ILE* 5.2 0.2 - - + -
93A ARG* 1.3 76.2 - - - +
95A ARG* 1.3 105.8 + - + +
96A GLY 3.3 2.0 - - - -
97A VAL* 2.9 19.7 + - - +
122A LEU* 3.6 41.9 - - + +
123A LEU* 3.8 17.5 - - + -
125A LEU* 5.4 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