Contacts of the strand formed by residues 53 - 60 (chain D) in PDB entry 2JG1
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 VAL 53 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MSE 3.9 7.1 - - - +
2D ILE* 3.4 11.7 - - + +
4D THR* 3.9 17.0 - - + -
43D THR* 4.0 21.8 - - + +
46D LEU* 3.8 30.1 - - + -
47D ALA* 4.0 26.7 - - + +
51D GLU* 3.3 11.9 + - + +
52D PRO* 1.3 74.6 - - - +
54D LEU* 1.3 64.8 + - - +
55D ALA 4.3 0.2 - - - -
76D ILE* 4.8 4.9 - - + -
77D LYS* 3.9 20.3 + - - +
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MSE 4.1 19.1 - - + -
2D ILE 2.9 10.5 + - - +
3D LEU* 3.3 16.1 - - + +
4D THR* 3.0 24.5 + - - -
53D VAL* 1.3 75.9 - - - +
55D ALA* 1.3 59.7 + - - +
77D LYS* 3.6 12.6 - - + -
78D HIS 3.7 35.2 - - - +
79D ALA* 3.8 6.1 - - + +
124D MSE 3.0 35.2 - - + -
127D LYS* 5.9 5.2 - - + -
128D VAL* 5.0 7.9 - - + -
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 4.5 0.4 - - - -
4D THR* 3.4 15.7 - - - +
40D LEU* 4.3 6.1 - - + -
43D THR* 4.0 18.8 - - + +
53D VAL 4.3 0.4 - - - -
54D LEU* 1.3 71.7 - - - +
56D SER* 1.3 56.5 + - - +
71D LEU* 4.2 7.2 - - + -
77D LYS 3.0 15.0 + - - +
78D HIS* 3.1 11.8 - - + +
79D ALA 2.8 31.5 + - - -
80D PHE* 4.1 14.0 + - + -
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Residues in contact with SER 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.7 20.9 - - - -
4D THR 2.9 12.4 + - - +
5D LEU* 4.0 10.8 - - - -
6D THR* 2.9 23.6 + - - +
54D LEU 3.9 0.2 + - - -
55D ALA* 1.3 72.9 - - - +
57D GLY* 1.3 63.2 + - - +
79D ALA 2.7 24.0 + - - -
80D PHE* 3.5 18.8 - - - -
117D PHE* 3.6 15.6 - - - -
120D HIS* 4.0 3.6 + - - -
121D PHE* 6.0 0.2 - - - -
124D MSE 4.1 6.9 - - - -
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Residues in contact with GLY 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 4.0 1.8 - - - +
6D THR 3.2 16.8 - - - -
7D LEU* 4.0 13.9 - - - -
56D SER* 1.3 82.4 + - - +
58D PHE* 1.3 58.2 + - - -
80D PHE* 3.4 7.0 - - - -
81D TYR* 2.8 32.6 + - - +
117D PHE* 4.0 6.3 - - - -
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Residues in contact with PHE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D THR 3.5 5.3 + - - -
7D LEU* 3.6 42.6 - - + +
9D PRO* 3.2 27.9 - - - +
57D GLY* 1.3 73.6 - - - -
59D ILE* 1.3 63.3 + - - +
81D TYR* 3.3 16.2 - + + +
83D ILE* 3.6 27.6 - - + -
87D THR* 4.6 0.3 + - - -
109D ILE* 4.0 34.3 - - + -
113D GLU 4.1 6.5 - - - -
117D PHE* 3.5 36.3 - + + -
138D PRO* 4.3 0.7 - - + -
141D LEU* 4.1 20.2 - - + -
145D TYR* 3.7 10.8 - + - -
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Residues in contact with ILE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D PRO* 4.3 11.4 - - + -
58D PHE* 1.3 80.4 - - - +
60D GLY* 1.3 58.2 + - - +
64D GLY* 3.7 31.9 - - - +
65D GLN* 4.4 7.9 - - - +
67D ILE* 4.5 7.9 - - + -
68D ALA* 4.7 6.5 - - + -
78D HIS* 5.8 0.4 - - - +
80D PHE* 3.7 51.6 - - + -
81D TYR 3.1 4.0 + - - +
82D ASN* 3.2 31.3 - - - +
83D ILE* 2.8 29.8 + - - -
87D THR* 3.5 7.6 - - - +
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Residues in contact with GLY 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ILE* 1.3 76.3 - - - +
61D GLY* 1.3 62.5 - - - -
62D GLU 3.9 0.3 + - - -
63D LEU 4.0 1.2 + - - -
64D GLY* 3.1 14.0 + - - -
82D ASN* 4.3 3.6 - - - -
83D ILE* 3.8 9.1 - - - +
85D GLY 3.1 23.6 - - - -
86D GLU* 3.6 0.7 - - - -
87D THR* 2.9 28.4 + - - +
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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