Contacts of the strand formed by residues 12 - 18 (chain C) in PDB entry 3SE3
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 CYS 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C SER* 1.3 81.3 - - - +
13C THR* 1.3 63.4 + - - +
14C PHE* 3.6 26.2 - - + -
27C TRP* 5.1 1.3 - - + -
28C GLU 3.1 6.1 - - - +
29C LEU* 3.3 28.3 - - + -
30C LYS* 5.9 0.2 - - - -
83C LEU* 4.8 6.1 - - + -
93C PHE* 4.8 0.9 - - - -
95C CYS* 2.1 57.2 - - - -
97C HIS* 4.6 5.4 - - - -
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Residues in contact with THR 13 (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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11C SER 4.4 0.4 + - - -
12C CYS* 1.3 72.9 - - - +
14C PHE* 1.3 71.5 + - - +
15C LYS* 5.6 2.9 - - + -
27C TRP* 3.2 5.4 - - - +
28C GLU* 2.7 56.6 + - - +
30C LYS* 5.2 6.4 + - - +
97C HIS* 5.8 0.9 - - - -
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Residues in contact with PHE 14 (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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12C CYS* 3.6 38.4 - - - -
13C THR* 1.3 81.8 - - - +
15C LYS* 1.3 60.9 + - - +
16C ILE* 4.3 0.5 + - - +
25C LEU* 4.5 12.3 - - + -
26C SER 3.5 4.7 - - - +
27C TRP* 4.0 14.1 - + + -
41C LEU* 5.3 1.8 - - + -
81C THR* 4.6 8.5 - - - -
83C LEU* 4.0 29.8 - - + -
95C CYS* 4.0 10.5 - - + -
96C SER 4.1 7.0 - - - -
97C HIS* 3.3 45.3 + + + +
99C PHE* 3.3 35.7 - + + -
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Residues in contact with LYS 15 (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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13C THR* 4.1 3.7 + - + -
14C PHE* 1.3 74.8 - - - +
16C ILE* 1.3 62.8 + - - +
17C SER* 3.3 23.5 + - - +
19C ARG* 4.6 10.1 - - - +
24C ILE 3.7 0.9 - - - +
25C LEU* 3.5 2.8 - - - +
26C SER* 2.9 51.4 + - - +
28C GLU* 4.4 16.1 + - - +
106C SER* 4.4 10.1 - - - -
108C GLU* 4.3 9.7 + - - -
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Residues in contact with ILE 16 (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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14C PHE 5.7 0.2 - - - +
15C LYS* 1.3 75.9 - - - +
17C SER* 1.3 66.3 + - - +
23C SER* 4.5 8.3 - - - -
24C ILE 3.5 24.7 - - - +
25C LEU* 3.8 21.1 - - + +
68C LEU* 5.2 2.0 - - + -
72C TRP* 5.0 11.7 - - + -
99C PHE* 4.1 15.3 - - + -
101C LEU* 5.3 7.9 - - + -
104C ASP* 3.2 39.0 - - + +
105C MET* 3.9 20.4 - - + +
106C SER* 3.3 19.9 + - - -
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Residues in contact with SER 17 (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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15C LYS* 3.3 30.1 + - - +
16C ILE* 1.3 74.1 - - - +
18C LEU* 1.3 56.5 + - - +
19C ARG* 4.1 13.3 + - - -
23C SER* 3.4 4.0 - - - -
24C ILE* 2.7 39.5 + - - -
26C SER* 5.5 0.5 + - - -
105C MET* 3.8 5.4 - - - +
106C SER* 3.3 20.0 + - - -
108C GLU* 3.8 16.8 - - - -
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Residues in contact with LEU 18 (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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17C SER* 1.3 74.3 - - - +
19C ARG* 1.3 60.4 + - - +
20C ASN 4.8 0.4 - - - +
21C PHE* 3.9 26.2 - - - +
22C ARG 3.2 14.8 - - - +
23C SER* 3.9 15.9 - - - +
105C MET* 3.7 22.4 - - + -
106C SER 2.8 13.2 + - - +
107C PHE* 4.4 18.8 - - + -
108C GLU* 2.9 31.9 + - - +
137C PHE* 4.3 17.5 - - + -
139C LEU* 5.3 6.1 - - + -
185C LEU* 5.8 4.9 - - + -
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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