Contacts of the strand formed by residues 10 - 17 (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 SER 10 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D PRO* 1.3 77.0 - - - +
11D VAL* 1.3 59.5 + - - +
12D ASP* 2.6 27.3 + - - -
34D THR 3.7 0.2 - - - +
35D ALA 3.7 0.2 - - - -
36D GLY* 2.6 43.2 + - - +
37D GLY* 4.4 1.7 + - - -
67D ILE* 3.9 7.5 - - - +
87D THR* 4.3 1.8 - - - -
88D ARG* 3.5 31.8 + - - -
90D CYS* 3.9 13.8 - - - -
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Residues in contact with VAL 11 (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* 1.3 70.9 - - - +
12D ASP* 1.3 62.6 + - - +
13D ILE* 4.9 2.7 - - + -
33D LYS* 4.7 11.9 - - + -
34D THR 3.5 3.4 - - - +
63D LEU* 3.6 45.3 - - + +
66D PHE* 3.7 39.3 - - + -
67D ILE* 4.2 7.4 - - + -
87D THR* 4.6 0.2 - - + -
88D ARG 2.9 11.5 + - - +
89D ASN* 3.0 35.4 + - - +
90D CYS 3.1 12.3 + - - +
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Residues in contact with ASP 12 (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* 2.6 30.5 + - - -
11D VAL* 1.3 70.1 - - - +
13D ILE* 1.3 63.2 + - - +
32D SER 3.6 1.6 - - - +
33D LYS* 3.2 5.9 - - - -
34D THR* 2.9 45.6 + - - +
36D GLY* 3.5 18.9 - - - -
37D GLY 4.4 1.6 + - - -
90D CYS* 3.4 17.2 - - - +
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Residues in contact with ILE 13 (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* 4.7 2.5 - - + -
89A ASN* 3.5 30.3 - - + +
91A ILE* 4.9 0.2 - - + -
11D VAL* 4.2 1.3 - - + +
12D ASP* 1.3 77.2 - - - +
14D SER* 1.3 61.8 + - - +
15D TYR* 3.5 32.5 - - + +
31D VAL* 3.5 20.4 - - + -
32D SER 3.6 2.0 - - - -
33D LYS* 3.9 17.3 - - + -
89D ASN* 3.7 25.4 - - - +
90D CYS 2.7 10.1 + - - -
91D ILE* 3.5 26.8 - - + +
92D ALA* 2.9 28.3 + - - +
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Residues in contact with SER 14 (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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12D ASP 4.2 0.6 + - - -
13D ILE* 1.3 72.5 - - - +
15D TYR* 1.3 63.5 + - - +
16D PRO* 3.6 10.2 - - - +
31D VAL* 3.7 6.9 - - - +
32D SER* 3.0 40.3 + - - -
92D ALA* 3.5 10.0 + - - +
94D LEU* 4.1 23.6 - - - +
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Residues in contact with TYR 15 (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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89A ASN* 4.2 1.7 - - - +
91A ILE* 3.3 38.8 - - + +
102A ILE* 3.7 34.2 + - + -
104A GLU* 2.5 31.9 + - + +
13D ILE* 3.5 19.4 - - + +
14D SER* 1.3 70.9 + - - +
16D PRO* 1.3 65.8 - - - +
17D LEU* 3.5 5.1 + - + +
28D VAL* 3.7 31.4 - - + -
31D VAL* 3.7 19.3 - - + -
91D ILE* 3.9 22.7 - - + -
92D ALA 2.9 11.7 + - - +
93D ILE* 3.5 5.7 - - + +
94D LEU* 2.8 26.5 + - - -
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Residues in contact with PRO 16 (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* 3.6 10.3 - - - +
15D TYR* 1.3 83.0 - - + +
17D LEU* 1.3 65.4 + - - +
28D VAL* 4.4 6.5 - - + +
30D GLU* 3.5 30.7 - - + +
94D LEU* 3.5 24.0 - - + +
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Residues in contact with LEU 17 (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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102A ILE* 4.5 6.7 - - + -
15D TYR* 4.1 10.3 - - + +
16D PRO* 1.3 75.4 - - - +
18D THR* 1.3 65.7 + - - +
19D ALA 3.5 20.2 - - - +
20D LEU* 3.8 22.9 - - + -
26D ASN* 4.3 20.9 - - + +
27D ARG 4.7 4.9 - - - +
28D VAL* 3.2 35.9 - - + -
93D ILE* 3.7 23.6 - - + -
94D LEU 2.8 17.7 + - - +
95D HIS* 3.6 7.9 - - + -
96D GLU 4.3 1.0 + - - -
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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