Contacts of the strand formed by residues 36 - 43 (chain A) in PDB entry 4JGN
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 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A PRO* 3.1 22.2 - - - +
35A LEU* 1.3 80.4 - - - +
37A PHE* 1.3 62.3 + - - +
38A LYS* 5.1 1.7 + - - -
51A TYR* 3.0 16.6 + - - -
52A LEU 3.1 14.1 - - - -
54A TYR* 3.6 15.3 - - - -
94A PHE* 3.7 8.3 - - - -
503E U 4.3 1.4 + - - -
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Residues in contact with PHE 37 (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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36A GLY* 1.3 75.6 - - - -
38A LYS* 1.3 71.1 + - - +
39A GLU* 3.7 28.9 - - + -
51A TYR* 3.4 4.4 - - - -
52A LEU* 2.9 54.2 + - + -
54A TYR* 3.8 12.8 - - + -
64A VAL* 3.5 45.1 - - + -
92A ILE* 3.7 24.2 - - + -
93A ARG 3.5 14.6 - - - +
94A PHE* 3.6 19.5 - - + -
119A LYS* 3.8 14.4 - - - -
123A LEU* 3.8 13.5 - - + -
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Residues in contact with LYS 38 (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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36A GLY 5.1 3.0 + - - -
37A PHE* 1.3 77.6 - - - +
39A GLU* 1.3 61.5 + - - +
50A ARG 3.3 7.9 - - - +
51A TYR* 3.4 25.0 - - + -
92A ILE* 3.3 5.0 - - - +
93A ARG* 2.9 54.1 + - + +
502E U 3.9 21.2 + - - -
503E U 3.0 31.4 + - - -
504E G 3.3 35.2 - - - +
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Residues in contact with GLU 39 (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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8A PHE* 3.4 24.3 - - + -
37A PHE* 3.7 13.5 - - + -
38A LYS* 1.3 76.2 - - - +
40A SER* 1.3 65.1 + - - +
49A LYS* 3.4 2.3 - - - +
50A ARG* 2.9 39.5 + - + +
52A LEU* 3.4 8.4 - - + +
67A SER* 2.5 28.2 + - - -
68A TRP* 3.1 5.1 + - - -
90A TYR* 2.6 33.3 + - + +
91A SER* 3.1 13.2 - - - +
92A ILE* 4.3 1.1 - - + -
119A LYS* 2.8 20.4 + - - -
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Residues in contact with SER 40 (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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8A PHE* 4.1 2.2 - - - -
39A GLU* 1.3 78.4 - - - +
41A TRP* 1.3 63.6 + - - +
42A GLY 4.3 0.2 - - - -
47A VAL* 3.9 15.9 - - - +
48A PHE 3.1 14.4 - - - -
49A LYS* 4.0 11.4 - - - -
89A THR 4.3 0.9 + - - -
90A TYR* 3.2 10.4 - - - -
91A SER* 2.5 55.4 + - - -
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Residues in contact with TRP 41 (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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7A PRO* 3.8 26.2 - - + -
8A PHE* 3.9 21.2 - + + -
40A SER* 1.3 71.8 - - - +
42A GLY* 1.3 58.5 - - - +
43A PHE* 3.7 22.2 - + + -
47A VAL* 3.4 3.3 - - - -
48A PHE* 2.9 36.8 + - - +
68A TRP* 3.4 39.2 - + - -
73A VAL* 3.5 22.3 - - + +
88A CYS* 5.1 0.7 - - + -
89A THR* 3.3 23.8 - - - -
90A TYR* 3.4 44.6 - + + -
108A LEU* 4.1 18.2 - - + -
111A LEU* 4.6 7.0 - - + -
112A CYS* 3.8 22.0 - - - -
115A ALA* 4.1 7.4 - - + -
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Residues in contact with GLY 42 (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* 4.3 0.4 + - - -
41A TRP* 1.3 74.3 - - - +
43A PHE* 1.3 69.3 + - - -
44A GLY 4.1 3.1 - - - -
46A VAL 3.3 7.9 - - - -
47A VAL* 4.1 14.5 - - - +
87A GLY 4.5 0.7 - - - -
88A CYS* 3.3 2.8 - - - -
89A THR* 2.7 41.5 + - - +
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Residues in contact with PHE 43 (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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7A PRO* 4.1 11.0 - - + -
41A TRP* 3.7 39.0 - + + -
42A GLY* 1.3 79.3 - - - -
44A GLY* 1.3 64.4 + - - +
45A LYS 3.2 0.3 + - - -
46A VAL* 2.8 27.0 + - - +
48A PHE* 3.8 35.4 - + - -
73A VAL* 4.0 19.3 - - + -
76A ALA* 4.2 2.9 - - + -
77A ALA* 3.7 42.6 - - + -
80A PHE* 4.1 22.4 - + + -
86A ILE* 3.9 13.9 - - + +
87A GLY 3.7 2.9 - - - -
88A CYS* 4.0 11.2 - - - +
108A LEU* 4.5 3.4 - - + -
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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