Contacts of the helix formed by residues 50 - 64 (chain A) in PDB entry 5MMB
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 PRO 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ASP* 3.9 35.2 - - - +
12A LEU* 3.8 18.8 - - + -
48A ILE 3.7 2.9 - - - +
49A PRO* 1.3 89.1 - - + +
51A GLN* 1.3 68.6 + - - +
52A SER* 4.3 11.2 - - - +
53A ASP* 3.0 39.4 + - - +
54A ARG* 3.3 8.1 + - - +
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Residues in contact with GLN 51 (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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9A ASP 5.6 0.8 - - - +
11A GLU* 4.7 13.0 + - - +
12A LEU* 5.2 1.8 - - - +
49A PRO 3.7 0.6 + - - -
50A PRO* 1.3 72.2 - - - +
52A SER* 1.3 62.7 + - - +
53A ASP 3.1 1.7 + - - -
54A ARG* 3.2 53.4 + - - +
55A GLN 4.5 1.9 + - - -
88A ASP* 5.4 6.9 + - - -
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Residues in contact with SER 52 (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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50A PRO* 4.3 12.5 - - - +
51A GLN* 1.3 78.6 - - - +
53A ASP* 1.3 66.7 + - - +
54A ARG 3.6 0.2 - - - -
55A GLN* 5.1 3.8 + - - +
56A LYS* 5.4 2.6 + - - +
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Residues in contact with ASP 53 (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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49A PRO* 4.2 11.6 - - + +
50A PRO* 3.0 34.6 + - + +
52A SER* 1.3 83.9 + - - +
54A ARG* 1.3 64.1 + - - +
55A GLN 3.4 1.8 - - - -
56A LYS* 3.4 13.5 + - - +
57A ILE* 3.2 28.2 + - + +
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Residues in contact with ARG 54 (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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11A GLU* 4.3 2.4 + - - -
12A LEU* 4.1 7.5 - - - +
24A TYR* 2.7 29.1 + - - -
48A ILE* 4.1 6.3 - - - +
49A PRO* 2.9 30.0 + - + +
50A PRO 3.3 11.6 + - - +
51A GLN* 3.2 42.5 + - - +
53A ASP* 1.3 76.3 - - - +
55A GLN* 1.3 66.7 + - - +
57A ILE* 3.2 7.2 + - - +
58A VAL* 3.0 29.9 + - - +
82A TRP* 3.6 61.6 - - + +
83A PRO* 4.1 6.7 + - - +
88A ASP* 4.9 8.9 + - - +
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Residues in contact with GLN 55 (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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51A GLN 4.5 2.2 + - - +
52A SER 5.1 3.5 + - - +
53A ASP 3.4 0.6 - - - -
54A ARG* 1.3 80.1 - - - +
56A LYS* 1.3 64.0 + - - +
57A ILE 3.3 0.2 + - - -
58A VAL* 3.3 6.5 + - - +
59A LEU* 3.0 27.9 + - + +
88A ASP* 6.3 1.1 - - - -
91A LYS* 5.6 6.1 + - - -
92A GLN* 4.0 27.8 + - - +
95A ARG* 6.2 0.6 - - - +
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Residues in contact with LYS 56 (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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52A SER 5.4 1.7 + - - +
53A ASP* 3.4 16.4 + - - +
54A ARG 3.3 0.6 - - - -
55A GLN* 1.3 81.9 - - - +
57A ILE* 1.3 58.5 + - + +
59A LEU* 3.7 11.8 - - + +
60A GLN* 3.1 54.2 + - + +
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Residues in contact with ILE 57 (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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49A PRO* 3.7 33.0 - - + -
53A ASP* 3.2 17.3 + - + +
54A ARG* 3.7 7.4 - - - +
55A GLN 3.2 0.6 - - - -
56A LYS* 1.3 76.5 - - + +
58A VAL* 1.3 66.3 + - - +
60A GLN* 3.3 11.5 + - - +
61A ALA* 3.1 23.5 + - + +
76A ILE* 4.1 17.3 - - + -
80A TYR* 3.7 48.9 - - + +
82A TRP* 4.2 4.3 - - + -
409A SO4 5.3 3.4 - - - +
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Residues in contact with VAL 58 (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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54A ARG 3.0 17.9 + - - +
55A GLN* 3.8 5.2 - - - +
57A ILE* 1.3 75.4 - - - +
59A LEU* 1.3 58.5 + - - +
61A ALA* 3.9 1.0 - - - +
62A HIS* 2.9 30.3 + - + +
72A THR* 4.4 3.4 - - + +
76A ILE* 4.0 14.6 - - + -
82A TRP* 3.8 24.5 - - + -
88A ASP* 3.7 26.0 - - + +
89A VAL* 3.8 20.0 - - + -
92A GLN* 3.6 27.8 - - + -
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Residues in contact with LEU 59 (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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55A GLN* 3.0 23.2 + - + +
56A LYS* 3.7 12.6 - - + +
58A VAL* 1.3 77.4 - - - +
60A GLN* 1.3 60.0 + - + +
62A HIS* 3.3 8.0 + - + +
63A ASN* 2.9 61.2 + - - +
92A GLN* 3.3 26.2 - - + +
96A CYS* 6.6 0.2 - - + -
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Residues in contact with GLN 60 (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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56A LYS* 3.1 53.9 + - + +
57A ILE* 3.3 10.9 + - - +
59A LEU* 1.3 78.1 - - + +
61A ALA* 1.3 61.9 + - - +
63A ASN* 3.6 9.7 + - - +
64A LEU* 3.4 22.4 + - - +
409A SO4 3.4 27.2 + - - +
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Residues in contact with ALA 61 (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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57A ILE* 3.1 13.0 + - + +
58A VAL 4.0 1.8 - - - +
60A GLN* 1.3 75.2 - - - +
62A HIS* 1.3 65.7 + - - +
63A ASN 3.5 0.3 + - - -
64A LEU* 3.5 25.2 + - + +
65A ALA 4.7 0.2 + - - -
67A THR* 4.4 6.4 + - - -
72A THR* 4.2 9.8 - - + +
75A LYS* 4.3 14.1 - - + +
76A ILE* 3.6 33.2 - - + +
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Residues in contact with HIS 62 (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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58A VAL* 2.9 21.6 + - + +
59A LEU* 3.8 9.4 - - + +
61A ALA* 1.3 76.7 - - - +
63A ASN* 1.3 67.9 + - - +
64A LEU 3.1 1.5 + - - -
65A ALA 3.6 0.5 + - - -
66A HIS* 2.7 41.0 + - - -
67A THR* 2.9 30.5 + - - -
72A THR* 3.8 16.0 + - + +
92A GLN* 5.5 7.0 - - + -
93A LEU* 3.3 22.9 - - + +
96A CYS* 3.3 11.9 - - + +
99A CYS* 3.3 13.0 - - + -
401A ZN 2.0 36.9 - - - -
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Residues in contact with ASN 63 (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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59A LEU* 2.9 43.6 + - - +
60A GLN* 4.2 5.8 - - - +
61A ALA 3.3 0.4 - - - -
62A HIS* 1.3 91.9 - - - +
64A LEU* 1.3 66.6 + - - +
65A ALA 3.3 0.6 + - - -
66A HIS* 3.5 28.9 + - - +
96A CYS* 5.1 0.7 - - - -
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Residues in contact with LEU 64 (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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60A GLN 3.4 18.3 + - - +
61A ALA* 3.6 19.1 - - + +
62A HIS 3.1 1.6 + - - -
63A ASN* 1.3 79.5 - - - +
65A ALA* 1.3 61.6 + - + +
75A LYS* 4.5 29.2 - - + +
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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