Contacts of the strand formed by residues 108 - 113 (chain L) 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 108 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7L ALA* 3.7 13.9 - - - +
8L GLY 3.5 8.4 + - - +
9L GLU 3.1 13.5 + - - -
11L PHE 3.2 28.7 - - - -
103L GLY 3.6 6.1 - - - -
104L LEU* 4.1 1.9 - - - +
106L GLY 4.1 0.2 - - - -
107L LYS* 1.3 72.4 - - - +
109L ALA* 1.3 58.2 + - - -
121L ARG* 2.9 14.2 + - - -
123L GLN* 5.1 2.3 + - - -
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Residues in contact with ALA 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ALA* 3.9 2.3 - - - +
12L ALA* 3.9 1.8 - - - +
76L ILE* 4.1 25.8 - - + -
101L ILE 4.8 0.2 - - - -
102L ALA* 3.4 2.9 - - - +
103L GLY 2.8 38.4 + - - +
105L ASP 4.2 4.5 - - - +
108L GLY* 1.3 71.7 - - - -
110L VAL* 1.3 69.6 + - - +
111L TYR* 4.2 6.3 - - + -
121L ARG* 3.2 30.1 - - - +
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Residues in contact with VAL 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L GLY 4.1 18.2 - - - +
6L ILE 3.8 6.7 - - - +
7L ALA* 3.5 30.5 - - + +
12L ALA* 4.7 0.9 - - + -
100L ILE* 4.2 16.4 - - + -
101L ILE 3.5 8.1 - - - +
102L ALA* 4.5 9.9 - - + -
109L ALA* 1.3 80.9 - - - +
111L TYR* 1.3 66.1 + - - +
121L ARG* 3.4 5.9 - - - +
122L GLU* 2.8 49.9 + - + +
123L GLN 4.3 0.9 - - - +
124L CYS* 4.7 1.1 - - - -
125L ARG* 4.5 15.0 - - + +
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Residues in contact with TYR 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L ILE* 3.7 44.2 - - + +
77L ASN* 3.6 24.1 + - + +
80L ALA* 3.6 21.3 - - + -
100L ILE* 3.4 4.0 - - - +
101L ILE* 2.8 48.3 + - + +
105L ASP* 5.9 0.3 - - - +
109L ALA* 4.2 5.2 - - + -
110L VAL* 1.3 79.2 - - - +
112L SER* 1.3 60.2 + - - +
113L PHE* 4.0 9.5 - - + -
119L TYR* 3.9 15.7 - + + -
120L GLU 3.5 13.2 - - - -
121L ARG* 3.7 39.3 + - + +
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Residues in contact with SER 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302K 3SD 3.5 13.3 - - - +
99L THR 3.4 8.7 - - - -
100L ILE* 4.0 4.3 - - - -
110L VAL* 4.5 0.6 + - - -
111L TYR* 1.3 76.0 - - - +
113L PHE* 1.3 64.7 + - - +
119L TYR* 3.4 4.9 - - - -
120L GLU 3.3 26.0 + - - -
122L GLU* 2.6 24.8 + - - -
125L ARG* 3.3 34.6 + - - -
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Residues in contact with PHE 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302K 3SD 4.5 5.2 - - - -
80L ALA* 3.3 45.8 - - + -
83L ILE* 3.8 16.4 - - + -
84L GLN 3.9 4.0 - - - -
87L LEU* 3.7 23.8 - - + -
98L HIS* 4.0 8.3 + - - +
99L THR* 2.8 47.9 + - + +
101L ILE* 4.2 11.2 - - + -
111L TYR* 4.0 21.3 - - + -
112L SER* 1.3 77.6 - - - +
114L ASP* 1.3 70.3 + - - +
117L GLY 4.2 6.5 - - - -
118L SER 3.3 5.8 - - - +
119L TYR* 3.4 26.2 - + + -
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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