Contacts of the helix formed by residues 26 - 34 (chain A) in PDB entry 3LP4
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 GLU 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLY* 3.4 18.2 - - - +
24A VAL 2.9 0.8 - - - -
25A GLU* 1.3 104.7 - - - +
27A GLY* 1.3 67.3 - - - +
28A PRO* 3.3 4.0 - - - -
29A THR* 2.9 38.9 + - - +
30A VAL* 3.2 14.5 + - + +
280A PRO* 4.4 13.0 - - + -
281A SER* 5.5 2.0 - - - +
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Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLY 4.4 0.2 + - - -
24A VAL 3.1 8.8 + - - -
26A GLU* 1.3 76.4 - - - +
28A PRO* 1.3 69.6 - - - +
30A VAL* 3.2 8.7 - - - +
31A LEU* 2.9 34.8 + - - +
98A GLY 3.3 14.6 - - - -
278A VAL* 3.9 15.0 + - - -
280A PRO* 4.6 0.6 - - - +
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Residues in contact with PRO 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY* 4.3 3.1 - - - -
13A ALA 3.8 11.0 - - - +
14A PRO* 3.8 13.9 - - + -
25A GLU 3.6 10.8 - - - +
26A GLU 3.3 4.5 - - - -
27A GLY* 1.3 87.1 - - - +
29A THR* 1.3 57.3 + - - +
31A LEU* 3.8 0.9 - - - +
32A ARG* 2.9 43.8 + - - +
52A ASP* 3.7 24.0 - - - +
97A LEU* 3.5 33.0 - - + +
98A GLY 3.3 11.2 - - - +
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Residues in contact with THR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLU 4.9 1.4 + - - -
26A GLU* 2.9 32.6 + - - +
28A PRO* 1.3 80.4 - - - +
30A VAL* 1.3 60.9 + - + +
32A ARG* 3.4 5.2 + - - +
33A LYS* 2.9 48.9 + - + +
52A ASP* 5.5 2.5 + - - -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLU* 3.7 9.0 - - + +
27A GLY* 3.2 14.8 - - - +
29A THR* 1.3 77.5 - - + +
31A LEU* 1.3 70.7 + - + +
33A LYS* 3.8 11.1 - - + +
34A ALA* 3.0 24.3 + - - +
278A VAL* 4.6 2.0 - - + -
280A PRO* 3.7 37.5 - - + -
289A VAL* 5.6 4.0 - - + -
293A VAL* 3.7 25.7 - - + +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLY* 2.9 30.3 + - - +
28A PRO 3.9 3.4 - - - +
30A VAL* 1.3 80.8 - - + +
32A ARG* 1.3 60.8 + - - +
34A ALA* 3.6 8.5 + - - +
36A LEU* 3.3 28.5 + - + +
97A LEU* 4.0 36.3 - - + -
98A GLY 4.5 4.5 - - - +
275A ILE* 4.1 15.9 - - + +
278A VAL* 4.6 9.2 - - + -
293A VAL* 4.0 20.0 - - + +
296A ALA* 3.8 30.1 - - + +
297A VAL* 4.3 9.5 - - + +
300A THR* 6.0 0.4 - - - +
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Residues in contact with ARG 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 4.0 7.9 - - + +
12A GLY* 3.6 15.6 - - - +
28A PRO* 2.9 30.7 + - - +
29A THR* 3.8 5.0 - - - +
31A LEU* 1.3 75.4 - - - +
33A LYS* 1.3 59.7 + - - +
34A ALA 3.1 1.8 - - - -
35A GLY* 2.8 21.1 + - - -
36A LEU* 3.8 7.7 + - + +
37A LEU* 4.0 25.7 + - + +
38A GLU* 4.3 3.1 - - - +
49A ASP* 2.9 40.3 + - - -
51A GLY 3.7 3.6 + - - -
52A ASP* 2.9 36.9 + - - -
97A LEU* 4.5 13.4 - - + +
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Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR* 2.9 38.7 + - + +
30A VAL* 3.8 11.0 - - + +
32A ARG* 1.3 72.6 - - + +
34A ALA* 1.3 59.0 + - - +
35A GLY* 2.8 10.5 + - - -
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A VAL 3.0 17.1 + - - +
31A LEU 3.7 8.3 - - - +
32A ARG 3.1 0.4 - - - -
33A LYS* 1.3 75.3 - - - +
35A GLY* 1.3 60.7 - - - +
39A LYS* 3.5 19.9 + - - -
293A VAL* 3.6 21.1 - - + -
294A ASN* 5.4 5.8 - - - +
297A VAL* 3.9 13.4 - - + +
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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