Contacts of the strand formed by residues 107 - 113 (chain J) in PDB entry 3SDI
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 LYS 107 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104J TYR* 4.0 3.8 - - - -
105J LYS* 3.0 55.2 + - + +
106J ASN* 1.3 82.0 - - - +
108J PRO* 1.4 73.7 - - + +
109J GLU* 4.6 8.6 - - + +
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Residues in contact with PRO 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ARG* 3.7 16.0 + - + -
8J VAL 3.6 13.2 - - - +
9J GLN 3.4 26.2 - - - +
10J ASP* 4.3 0.9 - - - -
11J SER* 3.5 26.7 - - - +
12J VAL* 3.6 20.4 - - + +
103J GLY 3.5 6.5 - - - +
104J TYR* 4.0 12.1 - - + -
106J ASN 4.5 0.9 - - - +
107J LYS* 1.4 90.6 - - + +
109J GLU* 1.3 68.7 + - - +
178J VAL 5.2 0.4 - - - +
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Residues in contact with GLU 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ARG* 4.6 3.6 - - - +
12J VAL* 3.4 4.6 - - - +
76J PRO* 3.9 16.0 - - + +
77J GLN* 3.9 7.6 + - - +
101J ILE 3.7 0.9 - - - +
102J GLY* 3.4 3.5 - - - -
103J GLY 2.8 40.1 + - - +
105J ASP* 3.8 43.1 + - - +
107J LYS* 4.6 6.4 - - + +
108J PRO* 1.3 84.4 - - - +
110J LEU* 1.3 60.4 + - - +
111J TYR* 2.7 41.0 + - + +
121J GLU* 4.9 11.0 - - - -
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Residues in contact with LEU 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J GLY* 3.6 32.1 - - - +
6J ILE* 3.9 3.4 - - - +
7J ARG* 4.2 7.9 - - + +
12J VAL* 3.8 22.4 - - + -
14J LEU* 3.9 17.5 - - + -
100J LEU* 4.6 8.5 - - + -
101J ILE 3.3 13.2 - - - +
109J GLU* 1.3 75.7 - - - +
111J TYR* 1.3 70.1 + - - +
112J GLN* 6.3 0.2 - - + -
121J GLU* 3.2 12.1 + - - +
122J LEU* 3.1 45.1 + - + +
123J PRO 3.9 3.6 - - - +
124J TYR* 3.7 14.1 - - - -
125J GLY* 3.8 7.4 - - - +
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Residues in contact with TYR 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J PRO* 3.9 14.6 - - + -
77J GLN* 3.5 20.1 - - + +
80J SER* 3.7 38.8 - - - -
99J VAL 4.0 0.3 - - - +
100J LEU* 3.3 10.3 - - - +
101J ILE* 2.8 49.7 + - + +
109J GLU* 2.7 43.4 + - + -
110J LEU* 1.3 78.2 - - - +
112J GLN* 1.3 61.6 + - - +
113J ILE* 4.7 3.4 - - + -
119J LYS* 4.0 24.7 - - + -
120J VAL 3.5 4.3 - - - +
121J GLU* 3.4 36.4 - - + +
122J LEU* 6.2 0.2 - - - -
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Residues in contact with GLN 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I VAL* 3.5 22.3 - - - +
100J LEU* 3.7 9.8 - - + +
110J LEU* 6.3 0.7 - - + -
111J TYR* 1.3 74.0 - - - +
113J ILE* 1.3 61.2 + - - +
118J THR 3.4 2.9 - - - +
119J LYS* 3.4 1.0 - - - -
120J VAL* 2.9 37.3 + - + +
122J LEU* 3.4 23.4 - - + +
125J GLY* 3.1 15.2 - - - -
126J ALA 3.0 43.7 - - - +
127J HIS* 3.5 26.0 + - + +
135J PHE* 4.1 3.1 - - - -
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Residues in contact with ILE 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80J SER* 3.8 26.0 - - - +
83J VAL* 4.0 15.9 - - + -
84J ARG* 4.3 7.6 - - + +
87J LEU* 3.5 17.9 - - + +
97J VAL 4.8 0.2 - - - +
99J VAL* 2.8 43.3 + - + +
101J ILE* 4.1 17.0 - - + -
111J TYR* 4.7 2.9 - - + -
112J GLN* 1.3 81.2 - - - +
114J ASP* 1.3 72.2 + - - +
117J GLY* 4.1 11.2 - - - -
118J THR 3.1 9.9 - - - +
119J LYS* 3.6 23.3 - - + -
127J HIS* 3.1 5.5 + - - -
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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