Contacts of the helix formed by residues 39 - 56 (chain F) in PDB entry 3V3K
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 SER 39 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F PHE 3.6 3.0 + - - -
38F LEU* 1.3 75.1 - - - +
40F PRO* 1.4 70.6 - - - +
41F GLU* 4.0 15.2 + - - +
42F LEU* 3.1 34.7 + - - +
43F GLN* 2.8 27.9 + - - +
112F ARG* 4.5 17.6 + - - +
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Residues in contact with PRO 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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38F LEU 4.6 1.1 - - - +
39F SER* 1.4 87.6 - - - +
41F GLU* 1.3 71.7 + - - +
43F GLN* 4.0 7.9 - - + +
44F ASP* 3.0 30.5 + - - +
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Residues in contact with GLU 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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39F SER* 3.2 14.9 + - - +
40F PRO* 1.3 92.0 - - - +
42F LEU* 1.3 61.5 + - + +
44F ASP* 3.9 4.8 - - - +
45F LYS* 3.2 26.2 + - - +
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Residues in contact with LEU 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F LEU* 4.1 15.9 - - + -
39F SER* 3.1 29.3 + - - +
41F GLU* 1.3 77.2 - - + +
43F GLN* 1.3 58.8 + - - +
45F LYS* 3.4 9.5 + - + -
46F LEU* 3.0 28.9 + - - +
72F PHE* 4.6 13.2 - - + -
112F ARG* 4.1 32.5 - - + +
113F ASP* 3.9 24.0 - - - +
116F PHE* 3.6 25.8 - - + -
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Residues in contact with GLN 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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38F LEU* 3.7 27.9 - - + +
39F SER 2.8 20.6 + - - +
40F PRO* 4.0 9.2 - - + +
42F LEU* 1.3 74.3 - - - +
44F ASP* 1.3 57.7 + - - +
46F LEU* 3.4 10.4 + - - +
47F ASP* 2.9 66.2 + - - +
123F LYS* 4.7 5.5 - - - +
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Residues in contact with ASP 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 PRO 3.0 19.7 + - - +
41F GLU* 3.9 5.6 - - - +
43F GLN* 1.3 77.4 - - - +
45F LYS* 1.3 58.2 + - - +
47F ASP* 4.1 5.3 - - - +
48F VAL* 3.1 39.9 + - - +
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Residues in contact with LYS 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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41F GLU 3.2 19.7 + - - +
42F LEU* 3.7 14.6 - - + +
43F GLN 3.3 0.2 - - - -
44F ASP* 1.3 73.4 - - - +
46F LEU* 1.3 64.6 + - - +
48F VAL* 3.7 6.6 + - - +
49F MET* 3.3 48.2 + - + +
68F GLU* 3.7 19.0 + - - +
72F PHE* 3.8 28.9 - - + +
116F PHE* 4.1 11.7 - - + -
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Residues in contact with LEU 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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38F LEU* 4.2 9.0 - - + -
42F LEU 3.0 17.6 + - - +
43F GLN* 3.7 10.3 - - - +
44F ASP 3.3 0.2 - - - -
45F LYS* 1.3 74.6 - - - +
47F ASP* 1.3 65.7 + - - +
49F MET* 3.1 5.6 + - - +
50F VAL* 2.9 47.3 + - + +
116F PHE* 3.6 25.8 - - + +
119F SER* 3.2 31.2 - - - +
120F LEU* 3.8 18.6 - - + +
123F LYS* 3.4 33.2 - - + +
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Residues in contact with ASP 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 GLN* 2.9 43.4 + - - +
44F ASP* 4.1 7.4 - - - +
46F LEU* 1.3 85.7 - - - +
48F VAL* 1.3 61.1 + - + +
50F VAL* 4.2 4.1 - - - +
51F SER* 3.2 24.1 + - - -
123F LYS* 4.1 6.6 + - - +
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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 ASP* 3.1 29.3 + - - +
45F LYS* 3.8 7.2 - - - +
46F LEU 3.2 0.2 - - - -
47F ASP* 1.3 77.8 - - + +
49F MET* 1.3 59.6 + - + +
51F SER* 3.0 19.4 + - - -
52F ILE* 3.1 36.6 + - + +
65F ILE* 5.8 0.2 - - + -
68F GLU* 5.9 3.8 - - - +
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Residues in contact with MET 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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45F LYS* 3.3 30.9 + - + +
46F LEU 3.1 8.5 + - - +
48F VAL* 1.3 79.3 - - + +
50F VAL* 1.3 58.4 + - - +
52F ILE* 4.0 0.7 - - - +
53F TYR* 2.9 32.4 + - - +
65F ILE* 3.7 42.2 - - + +
68F GLU* 3.2 33.0 - - + +
69F LEU* 4.2 15.5 - - + +
72F PHE* 6.4 0.4 - - + -
116F PHE* 3.7 18.6 - - + -
120F LEU* 3.6 27.6 - - + -
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Residues in contact with VAL 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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46F LEU* 2.9 43.9 + - + +
47F ASP* 4.2 6.1 - - - +
48F VAL 3.4 0.2 - - - -
49F MET* 1.3 76.0 - - - +
51F SER* 1.3 58.4 + - - +
53F TYR* 3.9 4.8 - - - +
54F SER* 3.0 29.0 + - - +
120F LEU* 5.1 10.1 - - + +
123F LYS* 3.6 40.2 - - + +
124F ILE* 6.1 4.0 - - + -
127F SER* 5.1 5.5 + - - +
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Residues in contact with SER 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 ASP 3.2 13.8 + - - -
48F VAL* 3.0 16.6 + - - -
50F VAL* 1.3 76.2 - - - +
52F ILE* 1.3 66.4 + - - +
54F SER* 3.2 6.9 + - - -
55F CYS* 3.2 34.3 + - - -
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Residues in contact with ILE 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* 3.1 39.3 + - + +
49F MET 4.0 0.4 - - - +
51F SER* 1.3 83.3 + - - +
53F TYR* 1.3 61.9 + - - +
55F CYS* 5.0 1.8 - - - -
56F ALA* 3.2 27.0 + - + +
61F GLU 5.3 6.5 - - - +
62F LEU* 4.4 0.6 - - + +
64F GLU* 5.7 7.9 - - + +
65F ILE* 3.4 39.7 - - + -
68F GLU* 6.0 1.1 - - - +
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Residues in contact with TYR 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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49F MET 2.9 19.2 + - - +
50F VAL* 3.9 6.3 - - - +
52F ILE* 1.3 79.6 - - - +
54F SER* 1.3 62.4 + - - +
56F ALA* 3.8 13.3 + - - +
62F LEU* 4.2 23.3 - - + +
65F ILE* 5.0 6.5 - - + +
124F ILE* 3.7 44.8 - - + +
127F SER* 4.3 21.1 - - - -
128F ARG* 3.5 25.1 + - + -
136F CYS* 3.0 37.2 - - - +
138F VAL* 4.1 18.8 - - + -
139F TYR* 4.5 0.3 - - - +
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Residues in contact with SER 54 (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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50F VAL* 3.0 17.9 + - - +
51F SER* 3.2 10.2 + - - -
53F TYR* 1.3 83.9 - - - +
55F CYS* 1.3 67.0 + - - +
56F ALA 3.6 5.7 + - - +
127F SER* 4.1 20.0 - - - -
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Residues in contact with CYS 55 (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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51F SER* 3.2 23.3 + - - +
52F ILE* 4.6 2.2 - - - +
54F SER* 1.3 82.5 + - - +
56F ALA* 1.3 62.9 + - - +
57F ARG* 3.0 32.4 + - - +
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Residues in contact with ALA 56 (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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52F ILE* 3.2 23.8 + - + +
53F TYR 3.9 5.7 - - - +
54F SER 3.4 8.7 - - - +
55F CYS* 1.3 80.2 - - - +
57F ARG* 1.3 63.5 + - - +
61F GLU* 3.9 21.3 - - + +
62F LEU* 3.5 27.1 - - + -
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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