Contacts of the strand formed by residues 88 - 95 (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 ARG 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ARG* 6.0 1.6 - - - +
33A LYS* 4.4 1.6 - - - +
8D ASN* 3.1 54.3 + - - +
9D PRO 3.2 15.5 + - - +
10D SER* 3.5 14.5 + - - -
11D VAL* 2.9 23.4 + - - -
63D LEU* 3.9 4.4 - - - +
86D GLU 3.5 2.7 + - - -
87D THR* 1.3 79.3 - - - +
89D ASN* 1.3 63.2 + - - +
90D CYS* 3.6 18.3 - - - -
103D LEU* 4.9 6.3 - - - +
104D GLU* 2.9 40.7 + - + +
105D GLN* 4.2 1.9 + - - +
106D GLY* 3.8 24.2 - - - -
107D PRO* 4.3 4.4 - - + +
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Residues in contact with ASN 89 (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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13A ILE* 3.5 19.9 - - + +
15A TYR* 4.1 6.3 - - - +
33A LYS* 2.9 19.9 + - - +
63A LEU* 6.2 0.2 - - - +
89A ASN* 5.0 3.5 + - - -
10D SER* 4.5 0.2 - - - -
11D VAL* 3.0 39.0 + - - +
13D ILE* 3.7 14.6 - - - +
63D LEU* 3.4 15.2 - - - +
88D ARG* 1.3 73.8 - - - +
90D CYS* 1.3 73.4 + - - +
91D ILE* 4.7 2.9 - - + -
104D GLU* 3.0 42.8 + - - +
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Residues in contact with CYS 90 (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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10D SER* 3.9 13.7 - - - -
11D VAL 3.1 7.6 + - - +
12D ASP* 3.4 17.3 + - - +
13D ILE 2.7 31.4 + - - -
88D ARG* 3.6 28.7 - - - -
89D ASN* 1.3 84.0 - - - +
91D ILE* 1.3 61.8 + - - +
102D ILE 3.5 8.1 - - - +
103D LEU* 4.0 19.5 - - + -
104D GLU 4.0 10.3 - - - -
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Residues in contact with ILE 91 (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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13A ILE* 5.1 0.4 - - + -
15A TYR* 3.4 38.4 - - + +
91A ILE* 4.1 17.5 - - + -
102A ILE* 5.3 0.7 - - + -
13D ILE* 3.5 31.9 - - + +
15D TYR* 3.9 25.6 - - + -
89D ASN* 4.7 3.1 - - + -
90D CYS* 1.3 81.9 - - - +
92D ALA* 1.3 62.4 + - - +
93D ILE* 3.9 20.6 - - + -
101D GLU* 3.2 7.5 - - - +
102D ILE* 2.9 44.0 + - + +
103D LEU* 4.7 1.7 - - - +
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Residues in contact with ALA 92 (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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13D ILE 2.9 11.0 + - - +
14D SER* 3.5 9.6 + - - +
15D TYR* 2.9 26.7 + - - +
91D ILE* 1.3 73.9 - - - +
93D ILE* 1.3 64.7 + - - +
94D LEU* 4.0 15.0 - - + -
99D GLN* 4.8 5.2 - - + -
100D THR 3.5 4.3 - - - -
101D GLU* 4.2 15.9 - - + +
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Residues in contact with ILE 93 (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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20A LEU* 5.7 0.2 - - + -
93A ILE* 4.2 21.3 - - + -
102A ILE* 3.9 24.7 - - + -
15D TYR* 3.5 6.5 - - + +
17D LEU* 3.7 30.3 - - + -
20D LEU* 4.3 13.0 - - + -
91D ILE* 3.9 16.8 - - + -
92D ALA* 1.3 76.1 - - - +
94D LEU* 1.3 63.1 + - - +
95D HIS* 3.4 22.9 - - + -
99D GLN* 3.4 2.8 - - - -
100D THR* 2.7 55.3 + - + +
102D ILE* 5.1 4.9 - - + -
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Residues in contact with LEU 94 (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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14D SER* 4.1 19.5 - - - +
15D TYR 2.8 13.3 + - - +
16D PRO* 3.5 16.2 - - + +
17D LEU 2.8 29.7 + - - +
92D ALA* 4.5 11.4 - - + -
93D ILE* 1.3 75.3 - - - +
95D HIS* 1.3 59.7 + - - +
98D GLN 3.5 5.2 - - - +
99D GLN* 3.7 34.8 - - + +
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Residues in contact with HIS 95 (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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22A LEU* 4.3 11.2 - - + -
17D LEU* 3.6 13.2 - - + +
19D ALA 4.5 1.1 - - - -
20D LEU* 3.6 46.4 + - + +
93D ILE* 3.4 29.6 - - + -
94D LEU* 1.3 74.8 - - - +
96D GLU* 1.3 72.6 + - + +
97D GLY 3.2 2.7 - - - +
98D GLN* 2.8 54.9 + - - +
100D THR* 2.7 28.1 + - - -
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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