Contacts of the strand formed by residues 107 - 113 (chain H) 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 GLY 107 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104H VAL* 3.4 1.4 - - - -
105H ASP* 2.9 34.5 + - - -
106H THR* 1.3 81.2 - - - +
108H SER* 1.3 59.8 + - - -
109H HIS* 3.4 8.9 - - - -
180H ILE* 3.9 21.1 - - - -
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Residues in contact with SER 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H LYS* 2.9 29.5 + - - +
8H PHE 4.9 0.9 + - - -
11H GLY* 3.5 40.3 + - - -
12H VAL* 4.5 1.6 - - - -
103H GLY 3.5 8.7 - - - -
104H VAL* 4.0 9.0 - - - -
107H GLY* 1.3 72.6 - - - -
109H HIS* 1.3 71.6 + - - +
180H ILE* 4.1 8.9 - - - +
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Residues in contact with HIS 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H LYS* 4.0 5.6 + - - +
12H VAL* 3.9 5.9 - - - +
76H VAL* 3.8 20.0 - - + -
77H VAL* 4.9 12.3 - - + +
101H VAL 4.6 0.7 - - - -
102H ALA* 3.3 4.2 - - - -
103H GLY 3.0 29.8 + - - +
105H ASP* 3.4 22.1 + - - -
106H THR* 3.1 30.9 + - - -
107H GLY 3.4 16.2 + - - -
108H SER* 1.3 82.8 + - - +
110H LEU* 1.3 62.4 + - - +
111H PHE* 3.6 29.6 - + + -
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Residues in contact with LEU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H GLY* 3.5 38.4 - - - +
6H VAL 3.9 1.6 - - - +
7H LYS* 4.0 14.8 - - + +
12H VAL* 4.0 9.0 - - + -
100H ILE* 3.8 20.2 - - + -
101H VAL 3.6 1.6 - - - +
102H ALA* 3.9 16.2 - - + -
109H HIS* 1.3 74.9 - - - +
111H PHE* 1.3 74.1 + - - +
121H VAL* 3.5 16.1 - - - +
122H GLY 3.4 28.6 + - - +
123H TYR 3.5 22.7 - - - +
124H TYR* 4.0 2.5 - - - +
125H LEU* 3.9 10.3 - - + -
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Residues in contact with PHE 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2191 TYR 4.7 0.4 - - - -
2201 GLY* 3.4 36.1 - - - -
76H VAL* 3.7 27.4 - - + -
77H VAL* 4.3 12.3 - - + -
80H LEU* 3.3 37.5 - - + -
100H ILE* 3.4 5.2 - - - +
101H VAL* 2.8 37.5 + - + +
109H HIS* 3.6 31.6 - + + -
110H LEU* 1.3 79.6 - - - +
112H SER* 1.3 61.6 + - - +
120H ASP 3.3 15.5 - - - +
121H VAL* 3.7 23.8 - - + -
125H LEU* 3.7 8.1 - - - +
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Residues in contact with SER 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H LEU 3.3 8.7 - - - -
100H ILE* 4.6 2.9 - - - -
111H PHE* 1.3 73.6 - - - +
113H ILE* 1.3 66.7 + - - +
114H HIS* 4.3 13.8 + - - -
118H SER 4.6 0.2 - - - -
119H THR* 3.2 8.0 - - - -
120H ASP* 3.0 50.9 + - - +
125H LEU* 3.7 19.4 - - - +
127H LEU* 4.5 15.7 - - - -
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Residues in contact with ILE 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H LEU* 3.5 28.3 - - + +
83H LEU* 3.6 37.7 - - + -
84H LYS* 4.5 9.9 - - + -
87H LEU* 3.9 25.1 - - + -
97H ALA 4.7 0.4 - - - -
98H TYR* 3.4 5.7 - - - +
99H LEU* 2.8 41.8 + - + +
101H VAL* 3.8 15.3 - - + -
112H SER* 1.3 78.1 - - - +
114H HIS* 1.3 70.6 + - - +
117H GLY 4.8 0.9 - - - -
118H SER 3.4 10.3 - - - +
119H THR* 3.8 9.2 - - + -
127H LEU* 4.3 0.7 - - - +
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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