Contacts of the strand formed by residues 99 - 104 (chain D) in PDB entry 2JG3
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 PHE 99 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D ARG* 3.7 43.1 - - + +
43D VAL 4.5 0.2 - - - -
44D LEU* 3.7 35.4 - - + -
68D VAL* 3.9 27.4 - - + -
93D TRP* 3.7 32.1 - + - -
95D PRO* 4.0 8.7 - - + -
97D GLU 3.8 12.8 - - - -
98D ALA* 1.3 77.6 - - - +
100D ASP* 1.3 62.5 + - - +
101D LEU 4.3 1.1 - - - +
102D ILE* 3.9 17.3 - - + -
153D LEU* 2.8 24.0 + - + +
154D LEU* 3.5 7.0 - - - +
155D LYS* 2.8 31.9 + - - +
158D GLY* 4.3 0.5 - - - -
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Residues in contact with ASP 100 (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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36D GLU 4.6 2.6 - - - +
37D ALA* 4.6 2.5 - - + -
38D PRO* 3.7 36.4 - - + +
41D GLY* 3.3 6.0 - - - -
42D ARG* 2.8 33.7 + - - +
99D PHE* 1.3 74.0 - - - +
101D LEU* 1.3 61.9 + - - +
154D LEU* 4.5 0.4 - - - -
155D LYS* 3.0 36.8 + - - +
158D GLY* 3.3 7.2 - - - -
159D VAL* 2.9 26.1 + - - +
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Residues in contact with LEU 101 (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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35D ALA* 3.9 19.1 - - + -
36D GLU 3.6 21.1 - - - +
37D ALA* 4.0 8.1 - - + -
42D ARG 3.1 5.0 + - - +
43D VAL* 3.3 20.3 - - + -
44D LEU* 2.8 26.0 + - - +
57D PHE* 3.3 43.3 - - + -
99D PHE* 3.5 0.5 - - - +
100D ASP* 1.3 79.6 - - - +
102D ILE* 1.3 76.8 + - - +
103D LEU* 4.4 8.3 - - + -
159D VAL* 3.2 27.1 - - + +
161D VAL* 4.4 2.7 - - + -
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Residues in contact with ILE 102 (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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44D LEU* 3.3 19.5 - - + +
46D PRO* 3.4 34.1 - - + -
99D PHE* 3.9 11.2 - - + -
101D LEU* 1.3 79.5 - - - +
103D LEU* 1.3 61.7 + - - +
150D ALA* 3.3 36.6 - - + +
153D LEU* 4.1 18.2 - - + -
154D LEU* 3.6 17.3 - - + -
159D VAL 2.8 10.7 + - - +
160D LEU* 3.0 9.3 - - - +
161D VAL 2.8 24.8 + - - +
162D PHE* 4.0 13.8 - - + -
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Residues in contact with LEU 103 (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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31D MET* 5.3 2.2 - - + +
32D VAL* 4.4 10.1 - - + +
35D ALA* 4.3 19.7 - - + -
43D VAL* 3.7 25.4 - - + -
44D LEU 2.9 18.4 + - - +
45D GLU* 3.4 25.6 - - - +
46D PRO* 3.4 1.9 - - - +
53D PHE* 3.8 43.1 - - + +
54D LEU* 4.8 3.8 - - + -
57D PHE* 4.4 10.8 - - + -
101D LEU* 4.4 7.9 - - + -
102D ILE* 1.3 76.7 - - - +
104D GLY* 1.3 59.6 + - - +
161D VAL* 3.1 19.1 - - + +
162D PHE* 4.0 5.2 - - - -
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Residues in contact with GLY 104 (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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31D MET* 3.2 7.7 - - - +
45D GLU* 4.6 4.9 - - - -
46D PRO* 4.8 2.5 - - - -
53D PHE* 3.6 23.1 - - - -
103D LEU* 1.3 76.9 - - - +
105D ASN* 1.3 60.3 + - - -
106D PRO* 3.8 0.2 - - - +
161D VAL 3.0 7.1 + - - -
162D PHE* 3.2 15.2 - - - -
163D VAL 3.2 23.0 + - - -
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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