Contacts of the helix formed by residues 20 - 31 (chain U) 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 ALA 20 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19U ASN* 1.3 77.0 - - - +
21U GLU* 1.3 60.8 + - - +
23U VAL* 3.8 4.2 + - - +
24U THR* 3.2 26.5 + - - -
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Residues in contact with GLU 21 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19U ASN* 3.1 1.1 - - - -
20U ALA* 1.3 77.8 - - - +
22U PHE* 1.3 58.0 + - - +
24U THR* 4.3 4.0 - - - -
25U GLN* 3.1 30.1 + - - +
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Residues in contact with PHE 22 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19U ASN* 2.9 28.9 + - + +
21U GLU* 1.3 77.1 - - - +
23U VAL* 1.3 65.4 + - - +
25U GLN* 3.3 4.0 + - - +
26U LEU* 3.0 24.5 + - - +
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Residues in contact with VAL 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19U ASN 3.1 9.8 + - - +
20U ALA* 4.4 4.0 - - - +
22U PHE* 1.3 78.8 - - - +
24U THR* 1.3 56.9 + - - +
26U LEU* 3.5 6.9 + - - +
27U ALA* 2.9 27.5 + - - +
53U GLU* 5.9 7.6 - - + -
63U LYS 6.0 1.6 - - - +
66U LEU* 5.4 12.3 - - + -
67U LEU* 5.9 5.6 - - + +
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Residues in contact with THR 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20U ALA 3.2 18.4 + - - -
21U GLU* 4.3 4.7 - - - -
22U PHE 3.2 0.6 - - - -
23U VAL* 1.3 76.9 - - - +
25U GLN* 1.3 60.2 + - - +
27U ALA* 3.2 8.4 + - - +
28U CYS* 2.9 28.9 + - - +
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Residues in contact with GLN 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21U GLU 3.1 22.7 + - - +
22U PHE* 3.8 4.3 - - - +
24U THR* 1.3 76.3 - - - +
26U LEU* 1.3 58.3 + - - +
28U CYS* 3.4 8.5 + - - +
29U LYS* 3.0 28.6 + - - +
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Residues in contact with LEU 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22U PHE 3.0 17.0 + - - +
23U VAL* 3.6 7.6 - - - +
25U GLN* 1.3 75.3 - - - +
27U ALA* 1.3 59.9 + - - +
29U LYS* 3.1 5.8 + - - +
30U TYR* 2.8 36.8 + - + +
45U VAL* 6.2 4.9 - - + -
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Residues in contact with ALA 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23U VAL 2.9 15.8 + - - +
24U THR* 3.4 11.9 - - - +
26U LEU* 1.3 76.5 - - - +
28U CYS* 1.3 58.3 + - - +
31U TRP* 2.9 16.2 + - + +
32U ALA* 2.5 40.4 + - + +
70U SER* 4.2 23.6 - - - +
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Residues in contact with CYS 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24U THR 2.9 15.7 + - - +
25U GLN* 3.6 9.0 - - - +
26U LEU 3.3 0.2 - - - -
27U ALA* 1.3 78.1 - - - +
29U LYS* 1.3 62.2 + - - +
31U TRP 4.9 0.3 + - - -
32U ALA* 3.8 12.0 + - + +
35U ILE* 4.4 16.9 - - - +
37U LYS 5.2 3.8 - - - +
38U LYS* 5.3 2.1 - - - +
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Residues in contact with LYS 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25U GLN 3.0 17.7 + - - +
26U LEU* 3.1 6.3 + - - +
28U CYS* 1.3 78.3 - - - +
30U TYR* 1.3 60.4 + - + +
38U LYS* 3.5 7.0 - - - -
39U SER* 2.9 33.2 + - - -
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Residues in contact with TYR 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U LEU* 2.8 19.9 + - + +
27U ALA* 5.5 0.2 - - - -
29U LYS* 1.3 77.8 - - + +
31U TRP* 1.3 62.7 + - + +
38U LYS* 3.7 16.2 - - - +
39U SER* 4.1 14.6 - - - +
40U PRO 5.6 2.9 - - - +
41U PHE* 6.4 1.1 - - - -
45U VAL* 5.7 8.7 - - + -
75U ASN 4.8 2.9 - - - +
76U TYR* 5.4 3.6 - - + +
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Residues in contact with TRP 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U ALA* 2.9 12.3 + - + +
28U CYS 4.8 0.4 + - - -
29U LYS 3.9 0.2 - - - -
30U TYR* 1.3 79.2 - - + +
32U ALA* 1.3 71.8 + - - +
33U PRO* 3.6 1.2 - - - +
38U LYS* 4.6 2.6 - - - +
70U SER 4.6 4.9 - - - +
71U GLN* 5.1 2.6 - - - +
72U TYR* 5.4 3.1 - - - -
75U ASN* 3.3 38.2 - - + +
76U TYR* 3.8 23.3 - - + -
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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