Contacts of the helix formed by residues 38 - 53 (chain F) in PDB entry 2F9K
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 ILE 38 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32F GLU* 3.4 44.0 - - + +
35F HIS* 3.2 20.6 - - + +
36F PRO 3.1 0.2 + - - -
37F GLU* 1.3 92.6 - - + +
39F GLY* 1.3 64.3 + - - +
40F ASP 3.2 2.5 - - - -
41F ALA* 3.1 16.2 + - + -
42F ILE* 2.9 32.0 + - + +
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Residues in contact with GLY 39 (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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35F HIS 5.2 0.4 - - - -
36F PRO* 3.0 16.2 + - - -
37F GLU 3.3 1.8 + - - -
38F ILE* 1.3 78.2 - - - +
40F ASP* 1.3 59.4 + - - +
42F ILE* 3.3 8.4 + - - +
43F ALA* 2.9 29.8 + - - +
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Residues in contact with ASP 40 (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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37F GLU 5.0 2.2 + - - +
38F ILE 3.2 0.6 - - - -
39F GLY* 1.3 78.0 - - - +
41F ALA* 1.3 57.1 + - - +
43F ALA* 3.5 7.2 + - - +
44F ARG* 3.0 26.0 + - - +
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Residues in contact with ALA 41 (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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38F ILE* 3.1 20.6 + - + +
40F ASP* 1.3 77.5 - - - +
42F ILE* 1.3 62.1 + - + +
44F ARG* 3.1 8.0 + - - +
45F LEU* 2.8 27.9 + - - +
134F LEU* 5.1 7.8 - - + +
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Residues in contact with ILE 42 (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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28F LEU 4.1 11.2 - - - +
29F THR* 3.5 43.0 + - + +
32F GLU* 3.7 28.9 - - + -
38F ILE* 2.9 34.4 + - + +
39F GLY* 3.6 10.5 - - - +
41F ALA* 1.3 78.4 - - + +
43F ALA* 1.3 55.7 + - - +
45F LEU* 3.3 15.8 + - + +
46F LYS* 3.0 26.5 + - - +
141F ARG* 4.6 2.5 - - - +
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Residues in contact with ALA 43 (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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39F GLY 2.9 17.3 + - - +
40F ASP* 3.7 8.5 - - - +
42F ILE* 1.3 73.8 - - - +
44F ARG* 1.3 65.4 + - - +
46F LYS* 3.3 9.9 + - - +
47F GLU* 3.0 22.3 + - - +
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Residues in contact with ARG 44 (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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40F ASP 3.0 14.7 + - - +
41F ALA* 3.1 12.1 + - - +
43F ALA* 1.3 75.5 - - - +
45F LEU* 1.3 58.8 + - - +
47F GLU* 3.0 21.8 + - - +
48F VAL* 2.8 37.2 + - + +
118F TRP* 4.1 9.0 - - - -
123F GLY 4.9 7.5 + - - -
124F VAL* 4.1 17.1 - - - +
127F ASP* 3.9 24.2 + - - +
131F ASP* 2.7 43.3 + - - +
134F LEU* 5.4 5.4 - - + -
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Residues in contact with LEU 45 (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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28F LEU* 4.2 9.0 - - + +
29F THR* 6.0 0.4 - - - +
41F ALA 2.8 12.5 + - - +
42F ILE* 3.5 19.5 - - + +
43F ALA 3.3 0.2 - - - -
44F ARG* 1.3 79.0 - - - +
46F LYS* 1.3 56.6 + - - +
48F VAL* 3.2 9.4 + - + +
49F LEU* 2.8 50.0 + - + +
134F LEU* 4.0 39.0 - - + +
135F LEU* 4.9 2.7 - - + +
138F CYS* 3.8 32.5 - - - -
141F ARG* 4.0 20.2 - - - +
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Residues in contact with LYS 46 (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 VAL* 4.0 20.7 - - + +
29F THR* 4.4 17.5 + - + +
42F ILE 3.0 14.4 + - - +
43F ALA* 3.4 12.3 - - - +
44F ARG 3.2 0.2 - - - -
45F LEU* 1.3 75.2 - - - +
47F GLU* 1.3 64.4 + - - +
49F LEU* 3.2 11.6 + - - +
50F GLU* 2.9 57.7 + - - +
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Residues in contact with GLU 47 (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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43F ALA 3.0 11.5 + - - +
44F ARG* 3.0 23.0 + - - +
46F LYS* 1.3 78.6 - - - +
48F VAL* 1.3 61.7 + - - +
50F GLU* 3.4 9.7 + - - +
51F TYR* 3.0 25.8 + - + +
118F TRP* 3.7 26.0 - - + -
121F LYS* 4.9 7.6 + - - -
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Residues in contact with VAL 48 (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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44F ARG* 2.8 23.7 + - + +
45F LEU* 3.5 13.7 - - + +
47F GLU* 1.3 76.8 - - - +
49F LEU* 1.3 62.5 + - - +
52F ASN* 3.0 45.7 + - - +
101F VAL* 5.9 0.2 - - + -
118F TRP* 3.8 14.8 - - + -
131F ASP* 3.5 44.9 - - + +
134F LEU* 5.8 1.3 - - + -
135F LEU* 3.8 29.4 - - + -
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Residues in contact with LEU 49 (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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21F PHE* 3.9 17.6 - - + -
24F ILE* 5.8 0.9 - - + -
25F VAL* 4.5 15.9 - - + -
28F LEU* 4.2 28.7 - - + -
29F THR* 5.7 1.6 - - - +
45F LEU* 2.8 42.9 + - + +
46F LYS* 3.5 10.8 - - - +
48F VAL* 1.3 75.2 - - - +
50F GLU* 1.3 60.0 + - - +
53F ALA* 2.8 36.1 + - + +
54F ILE 3.8 1.2 + - - -
94F LEU* 3.6 30.5 - - + -
135F LEU* 3.7 13.7 - - + -
138F CYS* 4.6 4.7 - - - -
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Residues in contact with GLU 50 (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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21F PHE* 4.5 14.4 - - + -
25F VAL* 4.5 5.6 - - + +
46F LYS* 2.9 56.2 + - + +
47F GLU* 4.0 6.9 - - - +
48F VAL 3.3 0.2 - - - -
49F LEU* 1.3 77.3 - - + +
51F TYR* 1.3 59.6 + - - +
54F ILE* 3.5 27.2 - - + +
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Residues in contact with TYR 51 (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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47F GLU* 3.0 18.5 + - + +
50F GLU* 1.3 81.1 - - - +
52F ASN* 1.3 66.3 + - - +
53F ALA 3.9 0.2 - - - -
54F ILE 3.9 4.9 - - - +
113F ARG* 5.5 0.3 + - - -
115F GLN* 2.9 58.5 + - + +
116F ILE* 2.5 50.7 + - - +
117F CYS* 5.1 0.2 - - - -
118F TRP* 3.4 42.8 - + + -
121F LYS* 3.5 24.7 - - + -
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Residues in contact with ASN 52 (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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48F VAL* 3.0 37.2 + - - +
51F TYR* 1.3 87.0 - - - +
53F ALA* 1.3 56.0 + - - +
54F ILE 3.4 1.3 - - - -
97F ALA* 3.6 13.1 - - + +
101F VAL* 3.6 23.5 - - + +
113F ARG* 2.7 27.4 + - - +
118F TRP* 3.3 46.3 + - - +
135F LEU* 4.4 10.8 - - + -
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Residues in contact with ALA 53 (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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21F PHE* 3.9 18.8 - - + -
49F LEU* 2.8 24.0 + - - +
52F ASN* 1.3 73.9 - - - +
54F ILE* 1.3 60.3 + - - +
58F TYR* 3.4 18.7 - - - -
90F TRP* 3.5 13.9 - - + -
93F GLU* 4.8 8.5 - - - +
94F LEU* 4.3 21.1 - - + -
97F ALA* 4.4 9.0 - - + -
113F ARG* 3.8 5.9 + - - +
135F LEU* 5.3 1.1 - - + -
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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