Contacts of the helix formed by residues 26 - 37 (chain H) in PDB entry 6FF7
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 26 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G ASP* 6.1 0.4 - - + -
8H SER* 3.7 26.8 - - - -
12H PRO* 5.8 6.1 - - + -
14H HIS 5.3 0.2 - - - -
15H PRO* 4.3 3.1 - - - -
16H CYS* 4.0 7.3 - - - +
25H TYR* 1.3 77.1 - - - +
27H ARG* 1.3 65.8 + - - +
28H ARG* 3.3 4.3 - - + +
29H LEU* 3.9 19.4 - - + +
30H ILE* 3.1 25.6 + - - +
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Residues in contact with ARG 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H HIS* 3.3 33.8 + - + +
16H CYS* 4.4 6.7 - - - -
26H GLU* 1.3 73.9 - - - +
28H ARG* 1.3 59.3 + - - +
30H ILE* 4.5 1.5 - - - +
31H GLU* 2.8 31.4 + - - +
52H LEU* 5.3 5.7 - - + +
53H ILE 4.8 7.0 - - - +
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Residues in contact with ARG 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G LYS* 5.8 0.9 - - - +
79G GLN* 3.6 38.6 - - + +
80G ASP* 4.7 2.8 - - + +
83G ASP* 4.6 2.8 - - - +
26H GLU* 3.3 3.7 - - + +
27H ARG* 1.3 77.2 - - - +
29H LEU* 1.3 61.1 + - - +
31H GLU* 3.8 5.3 - - - +
32H LYS* 2.9 32.9 + - - +
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Residues in contact with LEU 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G ASP* 3.7 27.2 - - + +
7H ILE* 4.1 26.9 - - + +
25H TYR* 5.5 1.1 - - + -
26H GLU* 3.5 21.9 + - + +
27H ARG 3.4 0.2 - - - -
28H ARG* 1.3 79.9 - - - +
30H ILE* 1.3 51.0 + - - +
32H LYS* 5.4 0.2 - - - -
33H TYR* 2.7 41.6 + - + +
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Residues in contact with ILE 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H CYS* 5.1 2.5 - - + -
17H VAL* 6.5 0.2 - - - -
25H TYR* 5.4 7.9 - - + -
26H GLU 3.1 15.6 + - - +
27H ARG 4.5 0.2 - - - +
29H LEU* 1.3 76.8 - - - +
31H GLU* 1.3 59.6 + - - +
33H TYR* 4.5 1.6 - - - -
34H ILE* 2.6 41.4 + - + +
51H GLN* 6.5 0.2 - - + -
52H LEU* 4.1 23.8 - - + +
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Residues in contact with GLU 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ARG 2.8 23.6 + - - +
28H ARG* 3.8 6.7 - - - +
29H LEU 3.3 0.6 - - - -
30H ILE* 1.3 77.0 - - - +
32H LYS* 1.3 51.8 + - - +
35H ALA* 2.6 37.1 + - - +
52H LEU* 5.5 1.5 - - - +
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Residues in contact with LYS 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G ASP* 5.1 15.3 - - + -
28H ARG 2.9 16.3 + - - +
29H LEU* 5.4 0.7 - - - -
31H GLU* 1.3 74.2 - - - +
33H TYR* 1.3 61.7 + - - +
35H ALA* 3.4 5.3 - - - +
36H GLU* 2.9 29.5 + - - +
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Residues in contact with TYR 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H LEU* 2.7 23.9 + - + +
30H ILE* 4.5 1.8 - - - -
32H LYS* 1.3 78.7 - - - +
34H ILE* 1.3 59.1 + - - +
36H GLU* 3.3 5.5 + - - +
37H ASN* 2.8 25.7 + - - +
39H THR 5.8 0.7 - - - +
41H PRO* 5.9 7.2 - - + -
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Residues in contact with ILE 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ILE* 2.6 29.0 + - + +
31H GLU 4.7 0.2 - - - +
33H TYR* 1.3 76.8 - - - +
35H ALA* 1.3 62.2 + - - +
37H ASN 3.3 19.8 - - - -
38H GLY* 3.5 10.6 + - - -
39H THR 4.5 14.7 + - - +
48H SER 5.7 5.8 - - - +
49H GLU* 6.4 1.3 - - - -
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Residues in contact with ALA 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H GLU 2.6 25.6 + - - +
32H LYS* 3.4 8.1 - - - +
33H TYR 3.1 0.6 - - - -
34H ILE* 1.3 77.2 - - - +
36H GLU* 1.3 66.1 + - - +
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Residues in contact with GLU 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H LYS 2.9 16.2 + - - +
33H TYR* 3.8 4.3 - - - +
35H ALA* 1.3 80.2 - - - +
37H ASN* 1.3 63.5 + - + +
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Residues in contact with ASN 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H TYR 2.8 16.7 + - - +
34H ILE* 3.3 6.1 - - - -
36H GLU* 1.3 83.6 - - + +
38H GLY* 1.3 66.5 + - - +
39H THR* 3.3 8.8 + - - +
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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