Contacts of the helix formed by residues 26 - 41 (chain K) in PDB entry 4B86
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 LYS 26 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K ASP* 3.0 9.4 + - - +
25K PRO* 1.3 88.3 - - + +
27K ALA* 1.3 67.1 + - - +
28K PHE* 3.0 3.1 + - - -
29K THR* 2.9 29.5 + - - +
30K GLU* 3.1 25.5 + - + +
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Residues in contact with ALA 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K LEU* 5.9 0.6 - - - +
20K TYR* 3.8 26.9 - - + -
21K ASP* 3.9 8.5 - - + +
24K ASP* 3.0 36.8 + - + +
25K PRO 3.7 0.2 - - - -
26K LYS* 1.3 77.0 - - - +
28K PHE* 1.3 61.2 - - - +
30K GLU* 3.7 10.6 - - - +
31K ILE* 3.4 28.1 + - + +
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Residues in contact with PHE 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K TYR* 4.4 7.0 - - + +
24K ASP 4.8 0.2 + - - -
25K PRO 5.5 0.2 - - - -
26K LYS 3.2 0.8 - - - -
27K ALA* 1.3 76.3 - - - +
29K THR* 1.3 70.8 + - + +
31K ILE* 2.9 11.6 + - + +
32K ASN* 2.9 43.4 + - + +
115K LEU* 3.8 44.6 - - + -
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Residues in contact with THR 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K PRO 4.9 1.0 + - - -
26K LYS* 2.9 24.5 + - - +
28K PHE* 1.3 85.9 - - + +
30K GLU* 1.3 54.6 + - - +
32K ASN* 3.7 11.7 - - + +
33K ARG* 2.9 45.9 + - - +
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Residues in contact with GLU 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K LEU* 3.5 32.4 - - + +
24K ASP* 3.3 23.0 - - - +
26K LYS* 3.1 24.9 + - + +
27K ALA* 3.7 12.7 - - - +
29K THR* 1.3 76.5 + - - +
31K ILE* 1.3 57.8 + - - +
33K ARG* 3.2 11.5 + - - +
34K LEU* 2.9 30.3 + - - +
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Residues in contact with ILE 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K LEU* 3.4 44.2 - - + +
17K VAL* 4.0 16.4 - - + +
20K TYR* 4.4 4.3 - - + -
27K ALA 3.4 15.9 + - - +
28K PHE* 2.9 10.6 + - + +
30K GLU* 1.3 79.3 - - - +
32K ASN* 1.3 58.6 + - - +
34K LEU* 3.2 5.0 + - - -
35K LEU* 2.9 53.2 + - + +
110K ILE* 5.4 5.8 - - + -
115K LEU* 3.5 32.5 - - + -
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Residues in contact with ASN 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K PHE* 2.9 34.6 + - + +
29K THR* 3.8 12.7 - - + +
30K GLU 3.4 0.2 - - - -
31K ILE* 1.3 77.3 - - - +
33K ARG* 1.3 55.5 + - - +
35K LEU* 4.9 4.1 - - - +
36K PRO* 3.3 23.4 - - - +
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Residues in contact with ARG 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K THR* 2.9 31.5 + - - +
30K GLU* 3.4 9.2 - - - +
32K ASN* 1.3 76.1 - - - +
34K LEU* 1.3 62.8 + - - +
36K PRO* 3.7 3.4 - - - +
37K TYR* 3.6 24.4 - - - -
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Residues in contact with LEU 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K LEU* 3.7 40.4 - - + +
12K SER* 3.6 30.3 - - - +
13K ALA* 4.0 10.8 - - + +
16K LEU* 3.7 27.6 - - + -
30K GLU 2.9 13.4 + - - +
31K ILE* 3.2 5.1 + - - +
33K ARG* 1.3 78.7 - - - +
35K LEU* 1.3 67.2 + - + +
37K TYR* 3.4 7.1 + - - +
38K PHE* 3.2 18.7 + - + -
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Residues in contact with LEU 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K ALA* 4.2 23.6 - - + -
17K VAL* 4.9 2.5 - - + -
31K ILE* 2.9 43.9 + - + +
32K ASN* 4.8 3.8 - - - +
34K LEU* 1.3 77.9 - - + +
36K PRO* 1.4 63.7 - - + +
38K PHE* 3.6 16.7 + - + +
39K ARG* 2.9 27.4 + - - +
103K TYR* 4.7 11.7 - - + +
106K LEU* 5.3 1.1 - - + -
107K CYS* 4.9 7.9 - - - -
110K ILE* 4.3 23.6 - - + -
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Residues in contact with PRO 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K ASN* 3.3 22.7 - - - +
33K ARG 3.7 6.5 - - - +
34K LEU 3.5 2.7 - - - -
35K LEU* 1.4 93.2 - - + +
37K TYR* 1.3 62.2 + - + +
39K ARG* 3.3 11.3 + - + +
40K GLN* 2.7 33.1 + - - +
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Residues in contact with TYR 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K LEU* 3.5 21.8 - - + +
33K ARG 3.6 20.6 - - - +
34K LEU* 3.4 6.2 + - - +
35K LEU 3.4 0.4 - - - -
36K PRO* 1.3 82.4 - - + +
38K PHE* 1.3 59.8 + - - +
40K GLN* 3.3 30.5 + - - +
41K SER* 3.1 21.8 + - - -
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Residues in contact with PHE 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K ALA 3.8 4.0 - - - -
9K LEU* 3.6 24.1 - - + +
10K TYR* 3.5 54.1 - + + -
13K ALA* 4.0 12.6 - - + -
34K LEU* 3.2 19.5 + - + +
35K LEU* 3.7 12.3 - - + +
37K TYR* 1.3 76.3 - - - +
39K ARG* 1.3 59.6 + - - +
41K SER* 2.7 22.6 + - - -
42K LEU* 3.7 23.8 + - + +
99K LEU* 5.0 0.7 - - + -
103K TYR* 3.2 45.1 - + + -
106K LEU* 4.3 18.4 - - + -
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Residues in contact with ARG 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K LEU 2.9 19.6 + - - +
36K PRO* 3.4 11.0 - - + +
38K PHE* 1.3 74.5 - - - +
40K GLN* 1.3 60.0 + - - +
42K LEU* 3.3 6.3 + - - +
43K SER* 2.7 47.5 + - - -
48K GLY 3.6 6.1 + - - -
49K HIS* 3.5 20.6 - - - +
50K LEU* 3.4 35.7 - - + +
103K TYR* 3.1 39.0 - - + +
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Residues in contact with GLN 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K PRO 2.7 19.7 + - - +
37K TYR* 3.4 35.0 - - - +
38K PHE 3.3 0.2 - - - -
39K ARG* 1.3 70.2 - - - +
41K SER* 1.3 56.8 + - - +
42K LEU 3.0 5.4 - - - -
43K SER* 3.0 33.7 + - - +
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Residues in contact with SER 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K ASN* 4.5 7.0 - - - -
6K ALA* 3.7 24.5 - - - +
9K LEU* 3.5 29.3 - - - +
37K TYR 3.1 5.8 + - - -
38K PHE* 2.7 21.7 + - - -
40K GLN* 1.3 74.9 - - - +
42K LEU* 1.3 63.0 + - - +
43K SER 3.6 0.9 - - - -
65K TYR* 3.7 28.1 - - - -
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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