Contacts of the strand formed by residues 116 - 124 (chain A) in PDB entry 3DJQ
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LYS* 4.1 30.5 - - + +
58A CYS* 3.6 6.1 - - - -
110A CYS* 3.1 0.5 - - - -
111A GLY 2.9 34.9 + - - +
114A PRO* 3.7 22.2 - - + +
115A SER* 1.3 79.5 + - - +
117A PRO* 1.3 78.5 - - + +
118A VAL* 3.6 2.3 - - + +
5B ALA* 3.7 31.0 - - + -
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Residues in contact with PRO 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 5.9 2.5 - - + -
54A VAL* 3.6 33.9 - - + +
55A LYS* 3.9 17.5 - - + +
58A CYS* 3.6 13.0 - - - -
108A VAL* 4.1 10.8 - - + -
109A ALA 3.3 8.1 - - - +
116A VAL* 1.3 89.9 - - + +
118A VAL* 1.3 62.5 + - - +
5B ALA* 4.0 9.2 - - - +
8B PHE* 3.3 44.9 - - + +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ASN* 4.7 3.6 - - - +
109A ALA* 2.8 26.1 + - + +
110A CYS 4.1 1.8 - - - -
111A GLY* 3.8 28.7 - - - +
116A VAL* 3.6 11.4 - - + +
117A PRO* 1.3 78.6 - - - +
119A HIS* 1.3 62.6 + - + +
4B ALA* 3.7 41.1 - - + +
5B ALA* 4.2 4.0 - - + +
7B LYS* 5.8 3.5 - - - +
8B PHE* 3.8 14.2 + - - +
12B HIS* 5.9 0.2 - - - -
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Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A CYS* 5.7 0.8 - - + -
67A ASN* 5.6 8.0 + - - -
72A CYS* 5.1 0.6 - - - -
108A VAL* 3.2 10.2 - - - +
109A ALA* 2.9 43.4 + - + +
118A VAL* 1.3 83.6 - - + +
120A PHE* 1.3 82.7 + - - +
121A ASP* 3.0 33.7 + - - +
125A UDP 3.6 32.9 + + - -
8B PHE* 3.6 8.7 - - - -
12B HIS* 5.2 1.8 - - - -
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A THR* 3.6 21.5 - - + -
47A VAL* 3.9 21.3 - - + -
106A ILE* 3.8 31.4 - - + -
107A ILE 4.1 1.3 - - - -
108A VAL* 4.3 11.9 - - + -
119A HIS* 1.3 88.4 + - - +
121A ASP* 1.3 62.5 + - - +
122A ALA 3.5 32.3 - - - -
123A SER* 4.1 5.8 - - - -
125A UDP 3.4 46.1 + + - -
8B PHE* 3.8 7.9 - + + -
12B HIS* 3.5 38.2 + + + +
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Residues in contact with ASP 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A THR 4.5 0.9 - - - +
65A CYS* 3.4 9.7 - - - +
66A LYS* 2.8 70.8 + - - +
67A ASN* 4.7 2.4 + - - +
72A CYS* 3.9 14.5 - - - -
107A ILE* 2.8 33.9 + - + +
108A VAL* 4.6 0.4 - - - -
119A HIS* 3.0 28.0 + - + +
120A PHE* 1.3 76.9 - - - +
122A ALA* 1.3 59.6 + - - +
125A UDP 4.2 7.8 + - - -
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LYS* 3.5 26.0 - - + +
106A ILE* 3.6 0.7 - - - -
107A ILE* 2.8 47.8 + - + +
120A PHE* 3.5 17.6 - - - -
121A ASP* 1.3 85.0 - - + +
123A SER* 1.3 63.0 + - - +
124A VAL* 6.2 0.2 - - + -
125A UDP 4.3 3.8 - - - -
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 3.8 24.8 - - - +
83A ASP* 4.8 6.5 + - - -
85A ARG* 5.8 1.7 + - - -
104A LYS* 2.8 38.4 + - - +
105A HIS 3.2 12.8 - - - -
106A ILE* 4.8 0.2 - - - -
107A ILE* 4.7 0.4 - - - +
120A PHE* 4.1 8.6 - - - -
122A ALA* 1.3 80.4 - - - +
124A VAL* 1.3 63.8 + - - +
125A UDP 4.3 8.1 + - - -
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLN* 3.9 25.4 - - + +
104A LYS* 3.3 23.0 - - - +
105A HIS* 2.9 61.2 + - + +
107A ILE* 4.4 12.8 - - + -
123A SER* 1.3 75.1 - - - +
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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