Contacts of the helix formed by residues 25 - 32 (chain B) in PDB entry 3ISL
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 ASP 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B VAL* 1.3 73.5 - - - +
26B PRO* 1.4 67.5 - - - +
27B ARG* 2.8 61.3 + - - -
28B VAL* 2.8 30.3 + - + +
29B LEU* 3.0 9.4 + - - -
203B SER* 4.1 6.8 + - - +
284B LEU* 3.6 19.6 - - + +
371B TYR* 3.5 33.0 - - + +
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Residues in contact with PRO 26 (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 VAL 3.3 4.9 - - - +
25B ASP* 1.4 88.1 - - - +
27B ARG* 1.3 57.0 + - + +
29B LEU* 3.8 14.8 - - + +
30B ARG* 3.0 43.4 + - - +
371B TYR* 3.4 31.9 - - + +
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Residues in contact with ARG 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 ASP* 2.8 49.6 + - - +
26B PRO* 1.3 75.2 - - - +
28B VAL* 1.3 59.0 + - - +
30B ARG* 3.5 47.1 - - - +
31B VAL* 3.8 8.8 + - - +
280B GLU* 4.7 7.9 - - - +
283B ARG* 5.2 8.5 + - - +
284B LEU* 3.6 38.6 - - + +
287B GLU* 4.1 12.3 + - - +
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Residues in contact with VAL 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 VAL* 3.5 19.1 - - + -
25B ASP* 2.8 19.7 + - + +
27B ARG* 1.3 71.1 - - - +
29B LEU* 1.4 66.5 + - - +
31B VAL* 3.1 25.5 - - - +
32B MET* 3.7 5.0 - - + +
202B LEU 5.6 0.2 - - - +
203B SER 4.4 8.5 - - - +
204B VAL* 4.7 1.1 - - + -
205B PRO* 4.2 5.8 - - + -
277B ALA* 3.7 32.5 - - + +
280B GLU* 4.2 3.4 - - + -
281B GLY* 3.5 33.0 - - - +
284B LEU* 4.0 15.5 - - + -
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Residues in contact with LEU 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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32A MET 4.1 2.0 - - - +
33A SER* 3.3 37.4 - - - +
34A THR 3.7 17.9 - - - +
35A PRO* 3.9 27.6 - - + -
36A VAL* 4.9 4.9 - - + -
273A THR* 5.0 0.2 - - - +
24B VAL* 3.7 43.5 - - + +
25B ASP 3.0 8.7 + - - +
26B PRO* 3.8 16.2 - - + +
28B VAL* 1.4 75.7 - - - +
30B ARG* 1.3 62.1 + - - +
32B MET* 3.1 33.2 + - + +
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Residues in contact with ARG 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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8A GLU* 5.5 6.2 + - - -
33A SER* 4.3 9.6 - - - -
26B PRO* 3.0 20.7 + - - +
27B ARG* 3.5 45.9 - - - +
29B LEU* 1.3 74.5 - - - +
31B VAL* 1.3 64.1 + - - +
32B MET 3.1 0.5 + - - -
33B SER* 3.1 26.2 + - - -
34B THR* 4.5 0.7 + - - -
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Residues in contact with VAL 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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9A LEU* 3.4 36.6 - - + -
27B ARG 4.0 5.4 - - - +
28B VAL 3.1 21.3 + - - +
29B LEU 3.3 1.0 - - - -
30B ARG* 1.3 81.1 - - + +
32B MET* 1.3 64.8 + - + +
33B SER 3.2 1.6 - - - -
34B THR* 2.7 33.4 + - - +
276B TYR* 4.0 16.2 - - + +
277B ALA* 4.1 5.4 - - - -
280B GLU* 3.7 33.4 - - + +
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Residues in contact with MET 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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29A LEU* 4.0 2.4 - - - +
32A MET* 3.2 61.2 - - + +
273A THR* 3.9 17.3 - - + +
28B VAL* 3.7 10.1 - - + +
29B LEU* 3.1 29.6 + - + +
30B ARG 3.1 2.8 - - - -
31B VAL* 1.3 80.4 - - + +
33B SER* 1.3 58.8 + - - +
34B THR 3.2 3.2 + - - +
205B PRO* 3.6 28.9 - - + -
273B THR* 3.8 26.3 - - + +
274B MET* 5.1 3.6 - - - +
276B TYR* 5.4 0.7 - - - -
277B ALA* 3.7 26.5 - - + -
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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