Contacts of the helix formed by residues 27 - 38 (chain a) 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 GLY 27 (chain a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26a THR* 1.3 70.9 - - - +
28a PRO* 1.3 68.0 - - - +
30a SER* 3.9 2.4 - - - -
31a VAL* 3.3 21.5 + - - +
35b SER* 3.3 33.6 - - - -
36b VAL 4.8 7.1 + - - +
37b ASP* 5.2 0.8 - - - +
43b GLN* 4.4 4.2 - - - +
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Residues in contact with PRO 28 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26a THR* 3.6 1.1 - - - -
27a GLY* 1.3 77.3 - - - +
29a LEU* 1.3 59.8 + - + +
31a VAL* 3.4 3.1 + - + +
32a LEU* 2.9 28.3 + - - +
35b SER 5.9 0.4 - - - -
36b VAL* 6.3 0.2 - - - -
41b ASN* 5.1 20.5 - - + +
42b MET 5.3 2.5 - - - -
43b GLN* 4.1 17.7 - - + -
63b LEU* 4.3 23.1 - - + -
64b ILE 5.7 0.7 - - - +
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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
----------------------------------------------------------
26a THR* 4.3 13.5 + - - -
27a GLY 3.5 0.4 - - - -
28a PRO* 1.3 80.1 - - + +
30a SER* 1.3 53.3 + - - +
32a LEU* 3.7 7.3 - - - +
33a THR* 2.6 37.9 + - - -
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Residues in contact with SER 30 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26a THR* 3.2 22.3 + - - -
27a GLY* 3.6 3.6 + - - -
28a PRO 3.3 0.4 - - - -
29a LEU* 1.3 78.2 - - - +
31a VAL* 1.3 58.1 + - - +
33a THR* 3.5 6.7 + - - -
34a GLN* 3.0 26.7 + - - +
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Residues in contact with VAL 31 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27a GLY 3.3 14.3 + - - +
28a PRO* 3.8 2.7 - - + +
30a SER* 1.3 74.8 - - - +
32a LEU* 1.3 60.1 + - - +
34a GLN* 2.7 27.9 + - - +
35a SER* 2.9 14.7 + - - -
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Residues in contact with LEU 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 PRO 2.9 19.0 + - - +
29a LEU* 3.7 8.1 - - - +
31a VAL* 1.3 75.8 - - - +
33a THR* 1.3 61.8 + - - +
35a SER* 3.5 6.6 + - - -
36a VAL* 3.0 22.7 + - - +
109a VAL* 5.6 10.3 - - + -
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Residues in contact with THR 33 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29a LEU 2.6 22.4 + - - -
30a SER* 3.6 8.1 - - - -
32a LEU* 1.3 71.9 - - - +
34a GLN* 1.3 53.5 + - - +
36a VAL* 3.0 10.3 + - - +
37a LYS* 2.6 35.9 + - - +
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Residues in contact with GLN 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 SER 3.0 14.2 + - - +
31a VAL* 2.7 18.3 + - - +
33a THR* 1.3 70.3 - - - +
35a SER* 1.3 60.5 + - - +
37a LYS* 3.1 23.7 + - - +
38a ASN* 3.2 10.2 + - - +
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Residues in contact with SER 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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31a VAL 2.9 13.9 + - - -
32a LEU* 3.9 6.5 - - - -
34a GLN* 1.3 73.8 - - - +
36a VAL* 1.3 59.2 + - - +
38a ASN* 3.2 8.4 + - - +
40a THR* 2.7 55.1 + - - -
111a ARG* 5.3 15.0 - - - -
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Residues in contact with VAL 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 LEU 3.0 14.7 + - - +
33a THR* 3.1 13.2 - - - +
35a SER* 1.3 72.3 - - - +
37a LYS* 1.3 67.1 + - - +
39a ASN* 3.0 15.3 + - - +
40a THR 4.7 4.5 + - - +
56a VAL* 4.0 37.7 - - + +
85g PRO* 5.2 12.3 - - + +
88g LYS* 6.1 0.7 - - - +
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Residues in contact with LYS 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 THR 2.6 16.3 + - - +
34a GLN* 3.1 17.7 + - - +
36a VAL* 1.3 73.8 - - - +
38a ASN* 1.3 55.7 + - - +
39a ASN 3.4 0.7 + - - -
85g PRO* 5.2 10.7 - - + +
88g LYS* 5.7 5.5 - - - +
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Residues in contact with ASN 38 (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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34a GLN 3.2 12.2 + - - +
35a SER* 3.2 6.5 + - - +
36a VAL 3.0 0.8 - - - -
37a LYS* 1.3 77.4 - - + +
39a ASN* 1.3 71.2 + - - +
40a THR* 3.3 4.6 - - - +
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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