Contacts of the helix formed by residues 25 - 38 (chain F) in PDB entry 6RIN
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 25 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F TYR* 3.7 18.3 + - + +
21F LEU* 3.6 27.9 + - + +
23F ARG 3.6 0.6 - - - -
24F GLU* 1.3 84.0 - - - +
26F ARG* 1.3 70.5 + - - +
27F PRO* 3.3 2.5 - - - +
28F GLU* 3.3 19.1 + - - +
29F VAL* 3.7 22.3 + - + +
54F ARG* 4.3 16.9 + - - +
58F ILE* 3.7 21.3 - - + -
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Residues in contact with ARG 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243D LEU* 3.2 56.9 + - + +
1244D GLN* 4.4 9.7 - - - +
21F LEU 3.3 13.0 + - - +
22F TRP* 4.4 28.8 - - + +
25F GLU* 1.3 80.7 - - - +
27F PRO* 1.3 64.0 - - + +
28F GLU 3.1 0.5 + - - -
29F VAL* 3.3 5.6 + - - +
30F THR* 2.7 34.7 + - - +
55F LEU* 2.9 52.2 + - - +
58F ILE* 3.7 18.9 - - + +
59F ASP* 4.7 11.1 + - - +
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Residues in contact with PRO 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F TRP 4.7 3.4 - - - +
23F ARG 3.2 28.5 - - - +
24F GLU* 4.1 2.0 - - - -
25F GLU 3.4 5.6 - - - +
26F ARG* 1.3 94.7 - - + +
28F GLU* 1.3 59.5 + - + +
30F THR* 3.1 11.3 - - - +
31F LYS* 2.8 35.4 + - + +
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Residues in contact with GLU 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F GLU 4.2 19.7 - - - +
25F GLU* 3.3 14.9 + - - +
26F ARG 3.2 1.0 - - - -
27F PRO* 1.3 76.3 - - + +
29F VAL* 1.3 68.9 + - + +
31F LYS* 3.1 9.6 + - - +
32F LYS* 2.9 27.1 + - + +
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Residues in contact with VAL 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F GLU* 3.7 22.2 + - + +
26F ARG* 3.3 8.3 + - - +
28F GLU* 1.3 77.4 - - + +
30F THR* 1.3 62.6 + - - +
32F LYS* 3.2 9.5 + - + +
33F VAL* 2.9 25.1 + - + +
51F ASN* 3.9 18.4 - - + +
54F ARG* 4.2 24.5 - - + +
55F LEU* 3.6 29.4 - - + -
58F ILE* 6.4 3.4 - - + -
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Residues in contact with THR 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242D ARG 4.4 8.3 - - - +
1243D LEU 4.7 5.3 + - - +
1244D GLN 5.1 0.9 - - - -
1245D GLY* 4.2 23.2 - - - +
26F ARG* 2.7 38.2 + - - +
27F PRO* 3.1 14.1 - - + +
29F VAL* 1.3 76.9 - - - +
31F LYS* 1.3 66.4 + - + +
33F VAL* 3.1 6.8 + - - +
34F THR* 2.9 27.5 + - - +
55F LEU* 4.6 6.7 - - - +
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Residues in contact with LYS 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599D LYS* 5.4 13.7 + - - +
27F PRO* 2.8 23.9 + - + +
28F GLU* 3.5 10.1 - - - +
30F THR* 1.3 76.1 - - + +
32F LYS* 1.3 57.8 + - + +
34F THR* 3.3 12.2 + - - +
35F TRP* 2.9 30.0 + - - +
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Residues in contact with LYS 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733D SER* 5.0 19.5 - - - +
28F GLU 2.9 19.1 + - - +
29F VAL* 3.5 12.1 - - + +
30F THR 3.2 0.2 - - - -
31F LYS* 1.3 77.7 - - + +
33F VAL* 1.3 57.1 + - - +
35F TRP* 3.3 21.3 + - + +
36F ALA* 2.9 30.0 + - - +
51F ASN* 4.6 20.1 + - - +
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Residues in contact with VAL 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929D GLN* 5.8 2.0 - - - +
1244D GLN 4.2 13.5 - - - +
1245D GLY 5.4 0.4 - - - +
29F VAL* 2.9 21.2 + - + +
30F THR* 3.7 4.3 - - - +
32F LYS* 1.3 73.8 - - - +
34F THR* 1.3 66.3 + - - +
36F ALA* 3.2 5.5 + - - +
37F ALA* 2.9 25.6 + - + +
48F TYR* 3.7 27.5 - - + +
51F ASN* 3.8 28.9 - - + +
52F LYS* 4.2 14.8 - - - +
55F LEU* 3.8 22.9 - - + -
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Residues in contact with THR 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497D GLU* 6.2 0.4 - - - +
599D LYS* 5.7 5.2 - - - +
1245D GLY* 2.8 36.0 + - - +
1246D VAL* 5.5 1.6 - - - -
1247D LYS* 5.3 13.2 - - + +
30F THR* 2.9 18.8 + - - +
31F LYS* 3.7 14.9 - - - +
33F VAL* 1.3 76.1 - - - +
35F TRP* 1.3 64.8 + - - +
37F ALA* 3.6 12.8 + - - +
38F SER* 3.9 5.7 + - - -
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Residues in contact with TRP 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598D LYS* 3.4 34.6 - - + +
599D LYS* 4.2 34.0 - - + +
726D ALA 5.7 0.7 - - - -
729D GLY* 3.0 36.2 + - - -
730D ALA 4.5 4.3 - - - -
732D GLY 4.5 14.8 - - - -
733D SER* 4.9 7.2 - - - -
31F LYS 2.9 14.9 + - - +
32F LYS* 3.4 27.4 - - + +
34F THR* 1.3 76.8 - - - +
36F ALA* 1.3 90.6 + - + +
38F SER* 2.9 23.0 + - - -
39F LEU* 4.2 14.6 + - + +
47F ASP* 3.2 29.4 - - + -
51F ASN* 5.4 0.9 - - - -
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Residues in contact with ALA 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F LYS 2.9 20.2 + - - +
33F VAL* 3.2 4.7 + - - +
35F TRP* 1.3 93.6 - - + +
37F ALA* 1.3 62.6 + - - +
39F LEU* 3.1 27.9 + - + +
41F ASP 5.6 0.3 - - - +
45F ASN* 4.3 6.2 + - - +
47F ASP* 4.6 5.6 - - + -
48F TYR* 4.1 32.9 - - + +
51F ASN* 4.7 2.0 - - - +
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Residues in contact with ALA 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929D GLN* 3.5 33.6 + - - +
1245D GLY 5.7 1.8 - - - +
1246D VAL* 5.9 0.9 - - + -
33F VAL* 2.9 17.4 + - + +
34F THR* 3.8 8.7 - - - +
35F TRP 3.0 0.4 + - - -
36F ALA* 1.3 78.7 - - - +
38F SER* 1.3 60.7 + - - +
39F LEU 3.0 11.1 + - - +
42F ARG* 4.9 10.8 + - - +
48F TYR* 4.7 12.5 - - + -
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Residues in contact with SER 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D ALA* 4.9 12.0 - - - +
499D ILE* 5.9 3.3 - - - +
501D VAL* 4.3 18.5 - - - +
598D LYS* 4.4 12.8 + - - -
34F THR 3.9 5.0 + - - -
35F TRP* 2.9 14.8 + - - -
37F ALA* 1.3 78.4 - - - +
39F LEU* 1.3 63.0 + - - +
40F GLY 3.9 0.3 + - - -
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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