Contacts of the strand formed by residues 26 - 33 (chain C) in PDB entry 3STJ
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 26 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C VAL* 4.5 6.3 - - + +
23C LEU* 3.0 8.1 + - - +
24C PRO 4.1 2.8 - - - +
25C ALA* 1.3 83.2 - - + +
27C VAL* 1.3 66.4 + - - +
67C GLY 3.3 15.7 - - - +
68C VAL* 4.5 3.8 - - + +
95C ASN 4.9 6.4 + - - -
127C ILE* 5.1 3.4 - - + -
144C VAL* 3.5 43.7 - - + +
145C GLY* 4.8 3.4 - - - -
152C GLN* 2.9 28.9 - - + +
189C GLY* 4.7 2.0 - - - -
190C ALA* 3.8 27.6 - - + +
192C LEU* 5.2 4.7 - - + -
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Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C PRO 4.4 2.2 - - - +
26C VAL* 1.3 80.1 - - - +
28C SER* 1.3 56.6 + - - +
29C VAL* 4.2 2.0 - - + -
66C SER* 3.3 8.0 - - - -
67C GLY* 2.7 53.8 + - - +
69C ILE* 3.6 23.6 - - + -
77C VAL* 3.9 16.8 - - + -
92C ILE* 3.9 23.1 - - + -
93C GLN 3.6 9.0 - - - +
94C LEU* 3.5 30.1 - - + -
146C ASN* 5.4 0.7 - - - -
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Residues in contact with SER 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 1.3 73.3 - - - +
29C VAL* 1.3 64.5 + - - +
30C ARG* 4.0 3.9 + - - +
64C LEU* 3.8 16.6 - - - +
65C GLY 3.7 4.5 - - - -
66C SER* 4.4 0.9 - - - +
91C SER 3.8 0.2 - - - +
92C ILE* 3.3 7.1 - - - +
93C GLN* 2.9 54.5 + - - +
146C ASN* 3.3 25.7 + - - -
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 4.2 1.3 - - + -
28C SER* 1.3 75.8 + - - +
30C ARG* 1.3 59.9 + - - +
31C VAL* 4.1 3.5 + - + +
63C GLY 4.0 0.2 - - - +
64C LEU* 3.5 4.9 - - - +
65C GLY 2.8 42.8 + - - +
66C SER 3.6 26.0 - - - +
67C GLY* 3.7 9.4 - - - +
77C VAL* 4.8 0.9 - - + -
79C THR* 4.5 2.9 - - - +
83C VAL* 4.0 9.1 - - + +
84C ILE* 3.7 30.7 - - + -
90C ILE* 4.0 16.2 - - + -
91C SER 3.6 2.5 - - - -
92C ILE* 4.0 16.8 - - + -
116C LEU* 4.2 5.8 - - + -
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Residues in contact with ARG 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C SER* 4.0 5.0 + - - +
29C VAL* 1.3 72.5 - - - +
31C VAL* 1.3 66.0 + - - +
32C GLU* 5.2 9.4 + - + +
62C GLU* 3.1 36.7 + - + +
63C GLY 3.6 9.0 - - - +
64C LEU* 4.4 17.8 - - + +
89C LYS 4.0 0.3 - - - +
90C ILE* 3.5 3.6 - - - +
91C SER* 2.8 56.5 + - - +
92C ILE 6.3 0.2 - - - -
93C GLN* 6.5 1.1 - - + -
99C GLU* 5.6 5.7 + - - -
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 4.3 7.2 - - + +
30C ARG* 1.3 79.9 - - - +
32C GLU* 1.3 66.0 + - - +
61C PHE* 3.8 24.7 - - + -
62C GLU* 3.3 6.6 - - - +
63C GLY* 2.8 38.5 + - - +
83C VAL* 3.8 26.0 - - + +
84C ILE* 3.9 12.3 - - + -
86C GLN 5.8 0.2 - - - +
87C ALA* 3.6 32.8 - - + +
89C LYS 3.4 2.7 - - - -
90C ILE* 3.9 12.3 - - + -
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Residues in contact with GLU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ARG* 5.2 10.6 + - + +
31C VAL* 1.3 82.1 - - - +
33C GLY* 1.3 59.0 + - - +
61C PHE 3.4 6.1 - - - +
62C GLU* 3.1 33.7 - - + +
87C ALA 3.7 0.2 - - - -
88C GLN* 2.8 24.6 + - - +
89C LYS* 2.9 44.3 + - + +
91C SER* 5.7 1.9 + - - +
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Residues in contact with GLY 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLU* 1.3 75.5 - - - +
34C THR* 1.4 60.0 + - - -
60C PRO* 3.3 23.4 - - - +
61C PHE* 3.2 25.7 + - - -
86C GLN 3.6 10.1 - - - -
88C GLN* 3.7 19.7 - - - +
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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