Contacts of the helix formed by residues 25 - 39 (chain A) in PDB entry 4KBQ
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A PRO* 1.3 75.8 - - - +
26A ALA* 1.3 60.1 + - - +
27A GLN* 3.6 4.1 + - - +
28A GLU* 3.1 38.7 + - - +
29A LEU* 3.0 28.9 + - - +
55A ARG* 3.5 26.2 - - - +
604C ASN* 3.9 12.2 + - - -
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Residues in contact with ALA 26 (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 SER* 1.3 75.3 - - - +
27A GLN* 1.3 58.2 + - - +
29A LEU* 3.4 0.9 + - - -
30A LYS* 3.0 25.6 + - - +
52A ALA* 3.6 26.8 - - - +
55A ARG* 3.1 26.2 - - - +
56A ASN* 4.1 13.2 - - + +
62A TYR* 3.3 29.4 + - + +
608C THR* 5.6 1.8 - - + +
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Residues in contact with GLN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 3.3 2.8 + - - +
26A ALA* 1.3 77.3 - - - +
28A GLU* 1.3 65.6 + - - +
30A LYS* 3.3 29.2 + - - +
31A GLU* 3.2 47.9 + - - +
55A ARG* 5.0 0.2 - - - +
62A TYR* 3.8 5.2 + - - -
604C ASN* 3.9 34.5 - - + +
607C ILE* 3.8 25.7 - - + +
608C THR* 4.0 17.8 + - - +
611C TYR* 3.7 15.3 + - - -
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PRO* 3.8 12.2 - - + +
25A SER* 3.1 38.6 + - - +
27A GLN* 1.3 78.4 - - + +
29A LEU* 1.3 60.1 + - - +
31A GLU* 3.3 15.3 + - - +
32A GLN* 3.1 21.1 + - - +
35A ARG* 5.4 0.7 + - - -
600C GLU* 4.1 11.5 - - - +
601C LYS* 3.7 22.6 + - - +
604C ASN* 4.0 17.3 + - - +
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Residues in contact with LEU 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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24A PRO* 4.3 25.1 - - + +
25A SER 3.0 22.2 + - - +
26A ALA* 3.7 4.7 - - - +
27A GLN 3.2 0.2 - - - -
28A GLU* 1.3 73.5 - - - +
30A LYS* 1.3 64.7 + - - +
32A GLN* 3.4 22.2 + - - +
33A GLY 3.1 16.8 + - - -
48A CYS* 3.7 20.6 - - - +
51A ARG* 3.9 59.2 - - + +
52A ALA* 3.9 13.0 - - + -
55A ARG* 5.7 2.7 - - + -
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Residues in contact with LYS 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 ALA 3.0 17.3 + - - +
27A GLN* 3.6 27.2 - - - +
29A LEU* 1.3 75.0 - - - +
31A GLU* 1.3 64.0 + - - +
33A GLY* 3.1 2.9 + - - -
34A ASN* 2.8 51.4 + - - +
49A TYR* 3.8 18.5 - - + -
52A ALA* 4.3 3.5 - - + +
61A VAL* 4.6 4.3 - - + -
62A TYR* 4.0 31.0 - - + -
65A ASN* 4.1 5.6 - - - +
611C TYR* 3.4 20.0 + - + -
646C ASP* 2.5 37.8 + - - +
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Residues in contact with GLU 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 GLN* 3.2 42.2 + - - +
28A GLU* 3.6 15.1 - - - +
29A LEU 3.3 0.2 - - - -
30A LYS* 1.3 80.0 - - - +
32A GLN* 1.3 65.4 + - - +
34A ASN* 3.3 9.0 + - - +
35A ARG* 3.1 42.3 + - - +
604C ASN* 5.1 2.6 - - - +
607C ILE* 6.0 0.5 - - - +
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Residues in contact with GLN 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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28A GLU 3.1 14.2 + - - +
29A LEU* 3.8 20.4 - - + +
30A LYS 3.3 0.4 - - - -
31A GLU* 1.3 74.4 - - - +
33A GLY* 1.3 62.9 + - - +
35A ARG* 3.2 28.9 + - + +
36A LEU* 3.1 33.2 + - + +
48A CYS* 3.5 21.2 - - - -
51A ARG* 4.6 6.7 + - - +
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Residues in contact with GLY 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 LEU 3.1 10.1 + - - -
30A LYS 3.1 4.0 + - - -
32A GLN* 1.3 77.4 - - - +
34A ASN* 1.3 55.3 + - - +
36A LEU* 3.3 5.0 + - - -
37A PHE 2.9 23.4 + - - -
45A ALA* 3.3 17.1 - - - +
48A CYS* 3.5 25.5 - - - -
49A TYR* 3.4 11.8 + - - -
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Residues in contact with ASN 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 LYS* 2.8 33.3 + - - +
31A GLU* 3.7 8.1 - - - +
33A GLY* 1.3 72.3 - - - +
35A ARG* 1.3 67.2 + - + +
37A PHE* 3.1 3.6 + - - +
38A VAL* 3.1 27.8 + - + +
49A TYR* 2.3 37.4 + - - -
65A ASN* 3.5 4.2 + - - -
645C VAL* 3.5 16.7 + - + +
646C ASP* 2.6 30.1 + - - -
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Residues in contact with ARG 35 (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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28A GLU 5.4 0.6 + - - -
31A GLU* 3.1 36.1 + - - +
32A GLN* 3.2 37.3 + - - +
34A ASN* 1.3 77.7 - - + +
36A LEU* 1.3 63.4 + - + +
38A VAL* 3.3 8.9 + - - +
39A GLY* 3.1 17.3 + - - -
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Residues in contact with LEU 36 (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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32A GLN* 3.1 28.9 + - + +
33A GLY 3.5 5.6 - - - +
35A ARG* 1.3 78.2 - - + +
37A PHE* 1.3 61.3 + - - +
39A GLY* 3.2 6.7 + - - +
41A LYS* 3.1 43.1 + - + +
44A GLU* 3.7 37.7 - - + +
45A ALA* 3.6 11.0 - - + -
48A CYS* 3.8 17.7 - - - -
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Residues in contact with PHE 37 (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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33A GLY 2.9 13.6 + - - +
34A ASN 3.1 8.5 + - - +
36A LEU* 1.3 75.8 - - - +
38A VAL* 1.3 64.4 + - + +
40A ARG* 2.9 21.8 + - - +
42A TYR* 3.5 40.8 + + - -
45A ALA* 3.7 7.2 - - + +
49A TYR* 4.1 1.6 - - - +
68A LEU* 3.5 40.4 - - + -
69A CYS* 4.0 13.9 - - - -
72A LYS* 4.4 11.7 - - + -
643C GLU 4.5 3.8 - - - -
644C GLU* 4.3 6.7 - - + -
645C VAL* 3.5 45.8 - - + -
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 3.1 15.0 + - + +
35A ARG* 3.3 11.4 + - - +
37A PHE* 1.3 84.0 - - + +
39A GLY* 1.3 56.8 + - - +
40A ARG* 3.1 14.6 + - - -
645C VAL* 5.6 3.6 - - + -
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Residues in contact with GLY 39 (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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35A ARG 3.1 12.8 + - - -
36A LEU* 3.2 4.9 + - - -
37A PHE 3.1 0.6 - - - -
38A VAL* 1.3 75.9 - - - +
40A ARG* 1.3 70.5 + - - +
41A LYS* 3.1 18.2 + - - +
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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