Contacts of the helix formed by residues 52 - 66 (chain F) in PDB entry 3MP4
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 52 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50F ILE* 4.3 0.4 + - - -
51F VAL* 1.3 81.7 - - - +
53F THR* 1.3 65.3 + - - +
54F PRO* 3.5 16.2 - - - +
55F VAL* 3.0 28.5 + - - +
56F LYS* 3.2 16.3 + - - +
87F ASP* 4.3 0.4 - - - -
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Residues in contact with THR 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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52F SER* 1.3 69.7 - - - +
54F PRO* 1.3 75.4 - - + +
56F LYS* 2.9 14.6 + - - +
57F ILE* 3.0 31.2 + - + +
87F ASP* 2.6 32.7 + - - +
90F GLU* 4.2 19.1 - - + +
91F VAL* 3.7 19.1 - - + -
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Residues in contact with PRO 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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52F SER* 3.5 16.4 - - - +
53F THR* 1.3 95.2 - - + +
55F VAL* 1.3 64.4 + - + +
57F ILE* 3.3 12.1 + - + +
58F LYS* 3.0 25.3 + - - +
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Residues in contact with VAL 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 VAL* 3.4 26.0 - - + -
52F SER* 3.0 31.0 - - - +
53F THR 3.1 0.4 - - - -
54F PRO* 1.3 80.9 - - + +
56F LYS* 1.3 61.5 + - - +
58F LYS 3.4 0.3 + - - -
59F LEU* 3.2 19.6 + - - +
305F PHE* 3.5 21.9 - - + -
306F ILE* 3.9 11.2 - - + -
309F ALA* 3.8 28.9 - - + -
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Residues in contact with LYS 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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40F PRO* 5.3 2.2 - - + +
44F LEU* 4.0 20.0 - - + -
50F ILE* 5.0 3.6 - - - +
51F VAL* 2.6 54.0 + - + +
52F SER 3.2 3.1 + - - +
53F THR 2.9 8.3 + - - +
55F VAL* 1.3 79.7 - - - +
57F ILE* 1.3 63.0 + - - +
59F LEU* 3.2 9.6 + - - +
60F ILE* 3.2 28.4 + - + +
84F GLN* 3.2 28.8 + - - +
85F MET* 4.1 19.1 - - + -
87F ASP* 3.5 27.1 + - - +
91F VAL* 4.2 17.9 - - + -
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Residues in contact with ILE 57 (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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53F THR* 3.0 33.8 + - + +
54F PRO* 3.7 10.3 - - + +
56F LYS* 1.3 76.1 - - - +
58F LYS* 1.3 62.4 + - - +
60F ILE* 3.4 2.9 + - - +
61F ASP* 3.1 34.8 + - - +
90F GLU* 4.3 3.8 - - + +
91F VAL* 4.5 7.9 - - + -
94F GLY* 3.3 42.0 - - - +
95F ILE* 3.8 18.4 - - + -
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Residues in contact with LYS 58 (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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54F PRO 3.0 16.7 + - - +
57F ILE* 1.3 75.4 - - - +
59F LEU* 1.3 61.4 + - - +
61F ASP* 3.4 8.0 + - + +
62F MET* 2.8 47.0 + - + +
305F PHE* 3.3 41.3 - - + -
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Residues in contact with LEU 59 (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 5.1 0.4 - - - -
40F PRO* 4.5 25.8 - - + -
44F LEU* 4.5 11.4 - - + -
55F VAL 3.2 13.4 + - - +
56F LYS* 3.4 9.9 - - - +
58F LYS* 1.3 75.8 - - - +
60F ILE* 1.3 53.3 + - + +
62F MET* 3.1 7.4 + - - +
63F LEU* 2.8 59.1 + - + +
260F VAL* 4.5 7.0 - - + -
263F LEU* 5.2 0.4 - - + -
302F ALA* 3.6 26.9 - - + +
305F PHE* 4.0 9.6 - - + -
306F ILE* 3.9 36.8 - - + -
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Residues in contact with ILE 60 (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* 3.9 22.2 - - + -
56F LYS* 3.2 14.3 + - + +
57F ILE 3.8 6.1 - - - +
58F LYS 3.4 0.2 - - - -
59F LEU* 1.3 73.2 - - + +
61F ASP* 1.3 53.7 + - - +
63F LEU* 3.2 8.8 + - - +
64F SER* 2.6 39.4 + - - +
71F ILE* 3.9 10.0 - - + +
73F THR* 3.4 39.0 - - + +
91F VAL* 3.9 9.6 - - + -
95F ILE* 3.7 36.6 - - + -
103F TYR* 4.1 16.6 - - + -
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Residues in contact with ASP 61 (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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57F ILE* 3.1 31.2 + - - +
58F LYS* 3.8 7.4 - - + +
60F ILE* 1.3 76.4 - - - +
62F MET* 1.3 54.6 + - + +
64F SER* 3.1 8.2 + - - -
65F GLU* 2.7 40.1 + - - +
94F GLY 5.0 0.3 - - - +
95F ILE* 3.9 5.5 - - - +
96F GLN* 3.0 62.3 + - - +
98F PHE* 4.4 2.0 - - + -
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Residues in contact with MET 62 (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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58F LYS* 2.8 38.5 + - + +
59F LEU 3.4 5.2 - - - +
61F ASP* 1.3 78.1 - - + +
63F LEU* 1.3 56.8 + - - +
65F GLU* 3.4 10.2 + - - +
66F ALA* 3.1 24.1 + - - +
298F LYS* 4.5 4.2 - - - +
301F GLU* 3.3 45.1 - - + +
302F ALA* 3.5 15.9 - - + +
305F PHE* 3.6 35.0 - - + -
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Residues in contact with LEU 63 (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* 3.8 26.0 - - + +
40F PRO* 4.0 11.9 - - + -
59F LEU* 2.8 35.0 + - + +
60F ILE* 3.5 6.7 - - - +
61F ASP 3.1 0.2 - - - -
62F MET* 1.3 73.8 - - - +
64F SER* 1.3 65.9 + - - +
65F GLU 3.1 0.2 - - - -
66F ALA* 3.1 16.9 + - + +
68F LEU* 3.5 22.4 + - + +
71F ILE* 3.6 18.8 - - + -
260F VAL* 3.8 29.6 - - + -
299F LEU* 4.4 11.2 - - + -
302F ALA* 3.7 21.1 - - + -
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Residues in contact with SER 64 (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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60F ILE* 2.6 25.6 + - - +
61F ASP* 3.4 6.6 - - - -
63F LEU* 1.3 76.4 - - - +
65F GLU* 1.3 61.7 + - - +
67F GLY* 3.3 11.1 + - - -
68F LEU 4.9 0.4 - - - -
71F ILE* 3.7 7.1 - - - +
96F GLN 4.5 0.5 + - - -
98F PHE* 3.4 35.6 - - - -
101F ILE* 3.7 19.6 - - - +
103F TYR* 3.2 28.0 + - - -
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Residues in contact with GLU 65 (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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61F ASP* 2.7 17.2 + - - +
62F MET* 3.4 13.0 - - - +
64F SER* 1.3 77.5 - - - +
66F ALA* 1.3 57.5 + - - +
67F GLY 3.3 1.2 + - - -
96F GLN* 5.2 1.9 + - - +
98F PHE* 3.0 34.5 - - - -
298F LYS* 3.1 35.9 + - + +
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Residues in contact with ALA 66 (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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62F MET 3.1 12.0 + - - +
63F LEU* 3.1 13.9 + - - +
65F GLU* 1.3 78.6 - - - +
67F GLY* 1.3 55.6 + - - +
68F LEU* 3.5 11.4 - - + -
294F VAL* 3.1 4.5 - - + +
295F ASN* 2.7 34.8 + - - +
298F LYS* 3.8 10.3 - - + -
299F LEU* 3.7 33.2 - - + +
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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