Contacts of the helix formed by residues 27 - 44 (chain L) in PDB entry 1EA4
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 SER 27 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L LEU* 1.3 76.8 - - - +
28L LYS* 1.3 65.4 + - - +
29L SER* 3.3 11.9 + - - -
30L ALA* 3.0 25.0 + - - +
31L MET* 2.8 21.0 + - - +
203V A 3.7 12.8 + - - -
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Residues in contact with LYS 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K LEU* 4.9 13.3 - - + +
7K ILE* 5.1 7.9 - - + -
14L LEU* 4.5 11.0 - - + +
17L LEU* 3.7 26.2 - - + -
18L GLU* 3.7 36.2 + - + +
21L ALA* 4.5 7.2 - - + +
26L LEU 3.9 0.2 + - - -
27L SER* 1.3 73.5 - - - +
29L SER* 1.3 64.9 + - - +
31L MET* 3.2 6.6 + - - +
32L ILE* 3.0 30.1 + - - +
203V A 5.1 5.3 + - - +
204V T 2.6 36.0 + - - +
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Residues in contact with SER 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K ILE* 3.2 19.6 - - - +
8K THR* 2.8 43.0 + - - +
9K LEU* 5.1 1.6 - - - +
27L SER* 3.3 8.9 + - - -
28L LYS* 1.3 79.9 - - - +
30L ALA* 1.3 61.6 + - - +
32L ILE* 3.5 5.5 + - - +
33L SER* 3.0 24.8 + - - -
203V A 3.3 18.3 + - - -
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Residues in contact with ALA 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L LEU* 3.8 18.8 - - + -
27L SER* 3.0 28.0 + - - +
29L SER* 1.3 74.7 - - - +
31L MET* 1.3 68.6 + - - +
33L SER* 2.8 9.9 + - - -
34L VAL* 2.8 26.9 + - + +
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Residues in contact with MET 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K LEU* 5.1 1.8 - - + -
39K TYR* 3.9 18.4 - - + +
17L LEU* 3.2 29.2 - - + -
20L MET* 3.8 39.7 - - + +
21L ALA* 3.9 9.2 - - + +
24L MET* 3.6 27.1 - - - +
26L LEU* 3.9 12.7 - - + +
27L SER 2.8 15.0 + - - +
28L LYS 3.4 8.7 - - - +
30L ALA* 1.3 70.7 - - - +
32L ILE* 1.3 58.6 + - - +
34L VAL* 3.0 22.1 + - + +
35L ALA* 2.9 27.7 + - + +
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Residues in contact with ILE 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K LEU* 5.0 1.3 - - + -
7K ILE* 3.8 39.3 - - + -
9K LEU* 4.7 3.4 - - + -
32K ILE* 4.1 28.7 - - + -
36K LEU* 4.4 10.1 - - + -
7L ILE* 4.5 8.3 - - + -
9L LEU* 5.4 0.2 - - + -
17L LEU* 3.9 24.9 - - + -
28L LYS 3.0 16.1 + - - +
29L SER* 3.5 7.4 - - - +
31L MET* 1.3 73.3 - - - +
33L SER* 1.3 68.4 + - - +
35L ALA* 3.2 8.0 + - + +
36L LEU* 2.8 43.7 + - + +
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Residues in contact with SER 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K THR 4.8 0.5 + - - -
9K LEU* 4.2 14.4 - - - +
10K SER* 4.9 1.6 + - - -
13K VAL* 3.9 28.3 - - - +
29L SER 3.0 15.4 + - - -
30L ALA* 2.8 15.7 + - - -
32L ILE* 1.3 73.9 - - - +
34L VAL* 1.3 57.4 + - - +
36L LEU* 3.6 5.6 - - - +
37L GLU* 2.8 36.3 + - - +
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Residues in contact with VAL 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K TYR* 4.0 18.8 - - + +
24L MET* 5.6 0.9 - - - -
26L LEU* 4.2 20.6 - - + -
30L ALA* 2.8 22.3 + - + +
31L MET* 3.1 19.5 - - + +
33L SER* 1.3 77.2 - - - +
35L ALA* 1.3 55.2 + - - +
37L GLU* 3.1 6.0 + - - +
38L ASN* 2.7 39.2 + - + +
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Residues in contact with ALA 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K ALA* 4.4 16.2 - - + +
36K LEU* 4.4 12.1 - - + +
39K TYR* 4.0 31.2 - - + +
20L MET* 6.0 0.4 - - + -
31L MET* 2.9 15.9 + - + +
32L ILE* 3.6 10.1 - - - +
34L VAL* 1.3 74.3 - - - +
36L LEU* 1.3 53.6 + - - +
38L ASN* 3.2 6.6 + - - +
39L TYR* 2.5 39.1 + - - +
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Residues in contact with LEU 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K LEU* 4.4 10.5 - - + -
13K VAL* 4.6 9.0 - - + -
16K ASN* 5.9 0.7 - - - -
17K LEU* 4.3 29.6 - - + -
20K MET* 4.4 22.5 - - + +
31K MET* 4.7 11.4 - - + -
32K ILE* 4.4 13.5 - - + -
35K ALA* 3.6 23.3 - - + -
32L ILE* 2.8 40.3 + - + +
33L SER* 3.6 4.0 - - - +
35L ALA* 1.3 71.7 - - - +
37L GLU* 1.3 66.2 + - - +
39L TYR* 3.0 6.8 + - + +
40L LYS* 2.8 24.9 + - - +
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Residues in contact with GLU 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K VAL* 3.3 30.1 - - + +
16K ASN* 5.2 2.4 + - - +
33L SER* 2.8 25.3 + - - +
34L VAL* 3.4 6.5 - - - +
36L LEU* 1.3 73.3 - - - +
38L ASN* 1.3 65.8 + - - +
40L LYS* 3.1 35.7 + - - +
41L LYS* 2.9 30.7 + - - +
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Residues in contact with ASN 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K ASN* 4.6 7.1 + - - -
39K TYR* 3.9 29.8 - - + -
34L VAL* 2.7 23.0 + - + +
35L ALA* 3.3 7.9 - - - +
37L GLU* 1.3 74.0 - - - +
39L TYR* 1.3 65.5 + - - +
41L LYS* 3.4 5.8 + - - +
42L GLY* 3.1 20.6 + - - -
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Residues in contact with TYR 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K MET* 3.8 23.6 - - + -
24K MET* 3.1 34.4 - - - +
31K MET* 3.9 18.6 - - + +
34K VAL* 3.8 17.0 - - + +
35K ALA* 4.0 20.4 - - + -
38K ASN* 3.4 33.0 - - - +
35L ALA 2.5 20.0 + - - +
36L LEU* 3.0 4.5 + - + +
38L ASN* 1.3 77.5 + - - +
40L LYS* 1.3 68.5 + - - +
42L GLY* 3.4 1.6 + - - -
43L GLN* 3.2 49.9 + - + +
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Residues in contact with LYS 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ASN* 3.1 44.7 + - - +
20K MET* 4.0 8.3 - - + -
36L LEU 2.8 11.0 + - - +
37L GLU* 3.2 43.0 + - - +
39L TYR* 1.3 78.6 - - - +
41L LYS* 1.3 76.4 + - - +
42L GLY 2.7 3.9 + - - -
43L GLN* 2.8 18.8 + - + +
44L GLU* 3.2 33.3 + - + +
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Residues in contact with LYS 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L GLU* 2.9 21.6 + - - +
38L ASN* 3.8 6.1 - - - +
40L LYS* 1.3 80.8 - - - +
42L GLY* 1.3 67.3 + - - +
44L GLU* 3.4 32.7 + - - +
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Residues in contact with GLY 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L ASN 3.1 12.2 + - - -
39L TYR* 3.7 4.0 - - - -
40L LYS 2.7 5.1 + - - -
41L LYS* 1.3 76.6 - - - +
43L GLN* 1.3 53.6 + - - -
44L GLU* 2.6 20.8 + - - -
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Residues in contact with GLN 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H LYS* 3.1 49.3 + - - +
24K MET* 5.5 2.4 - - - +
39L TYR* 3.2 46.1 + - + +
40L LYS* 2.8 15.5 + - + +
42L GLY* 1.3 67.6 - - - -
44L GLU* 1.3 63.2 + - + +
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Residues in contact with GLU 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L LYS* 3.5 38.3 - - + +
41L LYS* 3.5 31.0 + - - +
42L GLY 2.6 11.2 + - - -
43L GLN* 1.3 77.7 - - + +
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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