Contacts of the helix formed by residues 26 - 33 (chain B) 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 LEU 26 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B ARG* 3.9 11.0 - - - +
24B ILE 3.4 3.1 + - - +
25B SER* 1.3 70.5 + - - +
27B PHE* 1.3 68.9 + - - +
29B CYS* 3.0 13.8 + - - +
30B LEU* 3.4 14.7 + - - +
141B GLU* 3.9 18.2 - - + +
144B ARG* 3.8 24.2 - - - +
145B ALA* 4.7 5.6 - - + -
46C MET* 3.9 28.9 - - + +
78C ALA* 4.6 11.0 - - + -
80C VAL* 3.6 31.9 - - + -
98C ASN* 3.9 27.2 + - + +
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Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B SER* 3.1 11.1 + - - +
26B LEU* 1.3 79.4 - - - +
28B SER* 1.3 60.0 + - - +
29B CYS 3.1 4.7 + - - -
30B LEU* 3.2 37.7 + - + +
52C LEU* 4.9 8.1 - - + -
80C VAL* 3.8 8.5 - - + +
82C VAL* 4.5 23.6 - - + -
94C SER* 5.5 7.6 - - - -
96C SER* 3.4 31.4 - - - +
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 4.8 4.5 - - - +
25B SER* 3.1 28.3 + - - -
26B LEU 3.1 0.6 - - - -
27B PHE* 1.3 80.9 - - - +
29B CYS* 1.3 62.0 + - - +
30B LEU 3.5 0.7 - - - -
31B LYS* 5.0 4.0 + - - +
32B ASP* 4.8 1.7 - - - +
138B CYS* 3.3 11.6 - - - -
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Residues in contact with CYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.4 20.0 - - - -
25B SER 3.7 10.5 - - - +
26B LEU* 3.0 10.6 + - - +
28B SER* 1.3 77.7 - - - +
30B LEU* 1.3 67.2 + - - +
31B LYS 3.1 3.6 - - - -
32B ASP* 3.1 19.1 + - - +
33B ARG* 3.8 4.7 + - - +
138B CYS* 2.0 61.5 - - + +
141B GLU* 4.0 11.7 - - + -
142B VAL* 3.8 6.6 - - + +
46C MET* 4.7 4.5 - - + -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU 3.4 12.1 + - - +
27B PHE* 3.2 46.1 + - + +
28B SER 3.5 0.6 - - - -
29B CYS* 1.3 78.0 - - - +
31B LYS* 1.3 62.9 + - - +
33B ARG* 2.6 66.8 + - - +
44C THR* 4.2 17.7 - - + -
46C MET* 3.7 13.9 - - - -
49C PRO* 5.3 0.7 - - - +
52C LEU* 4.8 12.8 - - + -
80C VAL* 4.3 11.7 - - + -
82C VAL* 5.8 0.4 - - + -
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Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B SER 5.0 3.7 + - - +
29B CYS 3.1 0.6 - - - -
30B LEU* 1.3 79.9 - - - +
32B ASP* 1.3 66.6 + - - +
33B ARG 3.2 7.8 + - - +
133B LYS* 5.2 0.8 + - - -
49C PRO* 5.8 1.6 - - - +
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B SER 4.8 0.9 - - - +
29B CYS* 3.1 6.3 + - - +
31B LYS* 1.3 84.6 - - - +
33B ARG* 1.3 67.3 + - - +
129B TYR* 2.5 40.9 + - - +
133B LYS* 2.3 38.9 + - - +
136B SER* 4.7 3.0 + - - -
138B CYS* 3.4 31.4 - - + +
139B ALA 4.8 0.7 - - - +
142B VAL* 3.4 13.0 - - + +
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B CYS 3.8 3.3 + - - +
30B LEU* 2.6 57.3 + - - +
31B LYS* 3.2 4.9 - - - +
32B ASP* 1.3 81.7 - - - +
34B HIS* 1.3 61.2 + - - +
142B VAL* 3.9 7.9 - - + -
44C THR* 3.2 13.3 + - - +
45C ILE 3.2 26.8 + - - -
46C MET* 3.6 30.3 - - + +
48C LYS 3.4 5.1 + - - -
49C PRO* 3.7 36.8 + - + +
50C GLU 2.9 30.1 + - - -
51C ASP* 5.2 1.8 + - - +
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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