Contacts of the strand formed by residues 102 - 107 (chain D) in PDB entry 4JDA
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 ILE 102 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ILE* 4.0 4.3 - - - +
88D ARG* 3.1 29.4 + - + +
89D VAL* 3.2 22.8 + - + +
100D GLY 3.4 1.2 + - - +
101D THR* 1.3 74.0 - - - +
103D ARG* 1.3 60.2 + - - +
117D VAL* 5.0 9.0 - - + -
118D GLU 3.2 9.4 - - - +
119D ILE* 4.0 15.3 - - + -
135D LEU* 4.9 7.6 - - + -
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Residues in contact with ARG 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PHE* 2.6 77.5 + - + +
75D PRO* 3.7 18.8 - - - +
79D LYS* 3.6 23.6 - - - +
85D CYS* 3.6 21.1 - - - -
86D THR 3.6 3.8 - - - +
87D ILE* 3.7 19.1 - - + -
88D ARG* 4.2 2.5 - - - -
102D ILE* 1.3 75.2 - - - +
104D GLU* 1.3 60.9 + - - +
105D VAL* 3.9 12.7 - - + +
116D SER 3.7 0.5 - - - +
117D VAL* 3.2 6.0 - - - +
118D GLU* 2.8 47.5 + - + +
130D LEU* 5.9 0.4 - - - +
132D PHE* 3.8 22.4 - - - -
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Residues in contact with GLU 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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85D CYS* 3.6 1.4 - - - -
86D THR* 2.7 39.6 + - - +
88D ARG* 3.3 43.0 - - + +
103D ARG* 1.3 71.8 - - - +
105D VAL* 1.3 62.7 + - - +
106D SER* 4.1 1.0 + - - -
115D THR* 6.0 4.5 - - + -
116D SER 3.5 4.3 - - - +
117D VAL* 4.5 7.0 - - + +
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D PRO* 4.2 10.3 - - + -
82D ILE* 3.6 31.4 - - + -
84D SER 3.8 2.5 - - - -
85D CYS* 3.7 25.4 - - - -
103D ARG* 3.9 22.0 - - + +
104D GLU* 1.3 73.5 - - - +
106D SER* 1.3 65.4 + - - +
107D VAL* 4.9 5.8 - - + -
115D THR* 3.3 8.8 + - - +
116D SER* 2.6 51.3 + - - +
118D GLU* 5.8 1.8 - - + -
301D A9S 5.3 3.6 - - - +
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Residues in contact with SER 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D ILE* 3.6 2.1 - - - -
83D LYS* 2.8 35.1 + - - +
84D SER* 2.8 39.5 + - - +
104D GLU 4.1 1.1 + - - -
105D VAL* 1.3 75.1 - - - +
107D VAL* 1.3 57.3 + - - +
114D SER 3.6 8.1 - - - -
115D THR* 4.5 4.3 - - - -
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Residues in contact with VAL 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D PHE 3.4 15.3 - - - +
82D ILE* 4.7 0.7 - - + +
83D LYS* 4.1 6.9 - - - +
105D VAL* 4.8 9.0 - - + +
106D SER* 1.3 76.6 - - - +
108D VAL* 1.3 80.3 + - - +
109D SER* 3.8 0.9 + - - -
111D LEU* 3.8 13.2 - - + -
113D ALA* 3.4 23.7 - - + +
114D SER* 3.1 30.2 + - - +
115D THR* 4.0 7.6 - - - +
116D SER* 5.6 1.1 - - - -
301D A9S 3.7 32.3 - - + +
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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
------------------------------------------------------------
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