Contacts of the helix formed by residues 30 - 43 (chain K) 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 30 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26K PRO 4.3 7.2 + - - +
29K ARG* 1.3 79.0 - - + +
31K ALA* 1.3 61.6 + - - +
33K ALA* 3.2 5.0 + - - +
34K ALA* 2.9 27.9 + - - +
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Residues in contact with ALA 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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27K GLY 4.4 11.9 + - - +
29K ARG 4.4 1.6 - - - +
30K GLU* 1.3 78.5 - - + +
32K ALA* 1.3 56.4 + - - +
34K ALA* 2.7 28.4 + - - +
35K LEU* 3.0 12.0 + - - +
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Residues in contact with ALA 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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113I ALA* 5.4 9.2 - - + +
116I VAL* 5.1 7.1 - - + +
110J HIS 5.1 2.5 - - - +
114J CYS* 3.5 32.1 - - + -
28K VAL* 3.6 20.9 - - + +
30K GLU 3.5 0.2 - - - -
31K ALA* 1.3 77.9 - - - +
33K ALA* 1.3 57.3 + - - +
35K LEU* 3.4 7.7 + - - +
36K VAL* 2.9 28.5 + - - +
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Residues in contact with ALA 33 (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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29K ARG 2.9 26.6 + - - +
30K GLU* 3.2 6.6 + - - +
31K ALA 3.1 0.6 - - - -
32K ALA* 1.3 78.1 - - - +
34K ALA* 1.3 56.8 + - - +
36K VAL* 3.4 8.7 - - - +
37K GLU* 2.9 29.1 + - - +
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Residues in contact with ALA 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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30K GLU 2.9 10.9 + - - +
31K ALA* 2.7 19.2 + - - +
33K ALA* 1.3 70.1 - - - +
35K LEU* 1.3 64.8 + - - +
37K GLU* 3.2 7.1 + - - +
38K GLU* 2.9 23.3 + - - +
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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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112I ALA 5.3 2.0 - - - -
116I VAL* 3.9 22.9 - - + -
31K ALA 3.0 10.6 + - - +
32K ALA* 3.9 7.6 - - - +
34K ALA* 1.3 74.8 - - - +
36K VAL* 1.3 63.3 + - - +
38K GLU* 3.0 17.3 + - - +
39K GLU* 3.0 14.4 + - - +
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Residues in contact with VAL 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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109I GLN* 4.9 9.9 - - + +
112I ALA* 3.3 32.6 + - + +
113I ALA* 4.6 6.1 - - + +
32K ALA 2.9 19.3 + - - +
33K ALA* 3.4 10.5 - - - +
35K LEU* 1.3 76.1 - - - +
37K GLU* 1.3 62.5 + - - +
39K GLU* 3.1 6.2 + - - +
40K THR* 3.0 21.9 + - - -
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Residues in contact with GLU 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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33K ALA 2.9 18.2 + - - +
34K ALA* 3.2 7.4 + - - +
36K VAL* 1.3 76.1 - - - +
38K GLU* 1.3 57.8 + - - +
40K THR* 3.4 9.1 + - - -
41K ARG* 2.9 27.9 + - - +
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Residues in contact with GLU 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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34K ALA 2.9 13.3 + - - +
35K LEU* 3.0 12.8 + - - +
37K GLU* 1.3 73.9 - - - +
39K GLU* 1.3 65.7 + - - +
41K ARG* 3.0 10.0 + - - +
42K ARG* 3.0 19.9 + - - +
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Residues in contact with GLU 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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112I ALA* 4.4 18.2 - - + +
115I ARG* 6.0 4.3 - - + -
35K LEU 3.0 11.9 + - - +
36K VAL 3.6 7.0 - - - +
38K GLU* 1.3 75.2 - - - +
40K THR* 1.3 62.3 - - - +
42K ARG* 3.0 18.8 + - - +
43K TYR* 3.0 13.7 + - - +
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Residues in contact with THR 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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108I TYR* 5.2 14.8 - - - -
112I ALA* 5.5 0.4 - - - +
36K VAL 3.0 13.3 + - - -
37K GLU* 3.7 11.9 - - - -
39K GLU* 1.3 77.1 - - - +
41K ARG* 1.3 61.5 + - - +
43K TYR* 3.4 22.8 + - - +
44K ARG* 4.2 10.7 - - - +
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Residues in contact with ARG 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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37K GLU 2.9 15.6 + - - +
38K GLU* 3.0 12.3 + - - +
40K THR* 1.3 74.4 - - - +
42K ARG* 1.3 66.1 + - - +
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Residues in contact with ARG 42 (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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38K GLU 3.0 11.3 + - - +
39K GLU* 3.0 13.0 + - - +
41K ARG* 1.3 80.7 - - - +
43K TYR* 1.3 63.7 + - + +
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Residues in contact with TYR 43 (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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39K GLU 3.0 8.9 + - - +
40K THR* 3.4 14.8 + - - +
41K ARG 4.7 0.2 - - - -
42K ARG* 1.3 86.2 - - + +
44K ARG* 1.3 62.5 + - - +
45K PRO 4.1 2.0 - - - -
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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