Contacts of the helix formed by residues 13 - 22 (chain B) in PDB entry 1EJI
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 THR 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ASP* 2.9 46.1 + - - +
10B ARG 3.3 18.2 - - - +
11B ASP 2.6 6.4 + - - +
12B ALA* 1.3 75.1 - - - +
14B LEU* 1.3 72.5 + - + +
16B ALA* 3.4 16.9 - - - +
17B SER* 4.1 5.2 + - - -
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Residues in contact with LEU 14 (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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322A THR* 3.4 28.5 - - + +
323A GLU* 3.6 32.3 - - + +
326A ILE* 3.3 40.8 - - + -
10B ARG 5.5 0.9 - - - +
11B ASP* 2.7 16.1 + - - +
13B THR* 1.3 75.5 - - + +
15B TRP* 1.3 52.3 + - - +
16B ALA 2.6 5.8 + - - -
17B SER* 2.5 37.9 + - - +
18B HIS* 3.2 8.4 + - - -
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Residues in contact with TRP 15 (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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326A ILE* 3.5 26.8 - - + +
327A TYR* 4.7 8.7 - + - -
330A GLN* 3.6 39.6 + - + +
409A THR* 3.7 25.6 - - + -
410A SER 5.5 0.2 - - - -
412A GLY* 4.3 20.4 - - - -
414A LEU* 4.4 10.7 - - + +
11B ASP* 3.3 27.8 + - - -
12B ALA* 4.1 13.5 - - + +
14B LEU* 1.3 78.1 - - - +
16B ALA* 1.3 57.2 + - - +
18B HIS* 3.6 36.3 - + + -
19B GLU* 3.1 30.1 + - + +
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Residues in contact with ALA 16 (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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12B ALA 3.7 9.8 + - - +
13B THR* 3.4 15.4 + - - +
14B LEU 2.6 5.5 + - - -
15B TRP* 1.3 74.1 - - - +
17B SER* 1.3 59.9 + - - +
19B GLU* 3.0 24.5 - - - +
20B LYS* 3.1 10.4 + - - +
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Residues in contact with SER 17 (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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323A GLU* 3.2 28.7 + - - -
13B THR 4.2 5.2 + - - -
14B LEU* 2.5 22.1 + - - +
16B ALA* 1.3 68.0 - - - +
18B HIS* 1.3 64.9 + - - -
19B GLU 2.8 3.8 - - - -
20B LYS* 2.7 20.3 + - - +
21B MSE 2.8 14.2 + - - +
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Residues in contact with HIS 18 (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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260A ARG* 2.9 30.2 + - - -
323A GLU* 3.2 41.8 - - + +
326A ILE* 5.0 2.5 - - + -
327A TYR* 3.3 20.6 - + + +
410A SER* 4.3 8.5 - - - -
14B LEU 3.2 8.4 + - - +
15B TRP* 3.6 37.0 - + + +
17B SER* 1.3 78.8 - - - +
19B GLU* 1.3 64.7 + - - +
21B MSE 3.7 19.8 - - + +
22B LEU* 3.4 37.1 + - + +
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Residues in contact with GLU 19 (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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412A GLY* 6.1 0.7 - - - -
477A SER* 4.1 27.0 + - - -
15B TRP* 3.1 19.2 + - + +
16B ALA* 3.0 18.2 - - - +
17B SER 2.8 0.6 + - - -
18B HIS* 1.3 85.7 + - - +
20B LYS* 1.3 60.5 + - - +
22B LEU* 3.5 12.2 + - - +
23B SER* 3.4 12.7 + - - +
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Residues in contact with LYS 20 (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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16B ALA 3.1 7.7 + - - +
17B SER* 2.7 15.3 + - - +
19B GLU* 1.3 72.3 - - + +
21B MSE 1.3 53.5 + - - +
22B LEU 3.0 2.5 - - - -
23B SER* 2.7 15.8 + - - +
24B GLN* 2.7 60.6 + - + +
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Residues in contact with MSE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER* 4.1 1.9 - - - -
260A ARG* 3.6 28.0 - - - +
318A GLN* 4.0 42.4 + - + +
321A THR* 3.7 37.0 - - - +
323A GLU* 4.1 15.0 - - + +
324A PHE 4.5 2.2 - - - +
17B SER 2.8 19.0 + - - +
18B HIS* 3.7 20.0 - - + +
20B LYS* 1.3 73.4 - - - +
22B LEU* 1.3 64.4 + - + +
23B SER 3.5 0.7 + - - -
24B GLN* 3.9 28.5 + - - +
29B SER* 4.4 2.4 + - - +
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Residues in contact with LEU 22 (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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56A PHE 5.3 0.2 - - - +
58A SER* 3.7 23.8 - - - +
59A ARG 3.2 19.6 + - - -
260A ARG* 3.6 38.6 - - - +
318A GLN* 4.0 7.0 - - - +
410A SER* 4.0 7.4 - - - +
479A PRO* 3.7 32.8 - - + +
480A GLY 3.7 13.9 + - - -
18B HIS* 3.4 36.5 + - + +
19B GLU* 3.5 8.6 + - - +
20B LYS 2.9 1.6 + - - -
21B MSE 1.3 80.5 - - + +
23B SER* 1.3 58.8 + - - +
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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