Contacts of the helix formed by residues 55 - 72 (chain A) in PDB entry 3G33
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 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A VAL* 3.5 6.3 - - + -
45A PRO* 3.1 50.7 - - + +
53A GLY 4.2 0.4 - - - +
54A LEU* 1.3 85.0 - - + +
56A ILE* 1.3 67.3 + - - +
57A SER* 3.1 2.9 - - - +
58A THR* 2.8 36.1 + - + +
59A VAL* 3.2 9.5 + - - +
172A TYR* 3.8 21.3 - - + +
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Residues in contact with ILE 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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54A LEU 2.8 10.5 + - - +
55A PRO* 1.3 70.0 - - - +
57A SER* 1.3 62.9 + - - +
59A VAL* 3.3 6.0 + - - +
60A ARG* 3.0 49.7 + - - +
112D LYS* 3.2 42.6 - - + +
116D THR 5.1 1.6 - - - +
118D PRO* 3.2 38.1 - - + -
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Residues in contact with SER 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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55A PRO* 3.1 1.6 - - - +
56A ILE* 1.3 79.7 - - - +
58A THR* 1.3 64.2 + - - +
60A ARG* 4.0 6.8 - - - +
61A GLU* 3.3 34.5 + - - +
168A ARG* 3.4 53.1 + - - +
172A TYR* 4.3 13.2 + - - -
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Residues in contact with THR 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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44A VAL* 4.3 22.5 - - + +
55A PRO* 2.8 31.6 + - - +
57A SER* 1.3 76.7 + - - +
59A VAL* 1.3 64.3 + - + +
60A ARG 3.2 1.8 - - - -
61A GLU* 3.6 2.7 + - - +
62A VAL* 2.9 38.7 + - + +
94A VAL* 5.7 1.6 - - + -
168A ARG 4.2 5.6 + - - -
169A ILE* 4.1 25.9 - - + -
172A TYR* 4.0 15.6 - - - -
150D TRP* 4.8 8.1 - - + -
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Residues in contact with VAL 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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54A LEU* 3.7 37.2 - - + +
55A PRO 3.2 5.9 + - - +
56A ILE* 4.0 7.0 - - - +
58A THR* 1.3 79.3 - - + +
60A ARG* 1.3 61.7 + - + +
62A VAL* 4.2 1.0 - - - +
63A ALA* 3.2 22.9 + - + +
109D LEU* 4.7 7.6 - - + +
112D LYS* 5.3 11.4 - - + -
113D LEU* 4.1 8.7 - - + +
141D GLU* 5.1 2.2 - - - +
145D LEU* 4.3 11.0 - - + -
150D TRP* 4.1 22.5 - - + -
152D LEU* 4.2 23.6 - - + -
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Residues in contact with ARG 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 ILE* 3.0 35.6 + - - +
57A SER* 4.0 7.6 - - - +
59A VAL* 1.3 75.8 - - + +
61A GLU* 1.3 56.6 + - + +
63A ALA* 3.1 3.5 + - - +
64A LEU* 2.7 35.8 + - - +
168A ARG* 5.8 4.4 - - - +
112D LYS 3.1 24.3 + - - +
113D LEU* 3.8 28.3 + - + +
114D ARG 4.8 0.6 - - - -
115D GLU 2.6 38.0 + - - +
116D THR* 4.5 5.5 + - - +
118D PRO* 4.6 0.4 - - - +
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Residues in contact with GLU 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 SER 3.3 14.9 + - - +
58A THR 4.3 0.9 - - - +
60A ARG* 1.3 80.6 - - + +
62A VAL* 1.3 61.1 + - - +
64A LEU* 3.4 15.4 + - + +
65A LEU* 3.2 29.6 + - - +
165A GLY 3.3 20.1 - - - +
167A ALA* 3.5 8.6 + - - +
168A ARG* 3.1 53.6 + - - +
169A ILE* 3.7 16.4 - - + +
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Residues in contact with VAL 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 THR* 2.9 35.9 + - + +
59A VAL 4.2 0.2 - - - +
61A GLU* 1.3 76.3 - - - +
63A ALA* 1.3 62.0 + - - +
65A LEU* 3.5 9.3 + - - +
66A ARG* 3.2 22.9 + - - +
79A LEU* 4.1 5.1 - - + +
82A VAL* 4.1 17.0 - - + -
94A VAL* 5.4 5.4 - - + -
96A LEU* 4.6 11.2 - - + -
169A ILE* 4.3 16.8 - - + -
150D TRP* 3.5 43.5 - - + -
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Residues in contact with ALA 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 VAL* 3.2 21.2 + - + +
60A ARG 3.1 4.4 + - - +
62A VAL* 1.3 74.3 - - - +
64A LEU* 1.3 65.0 + - - +
66A ARG* 3.5 2.9 + - - +
67A ARG* 3.1 22.5 + - - +
113D LEU* 3.9 18.8 - - + -
150D TRP 3.5 21.1 - - - +
151D ASP* 4.9 0.9 - - - +
152D LEU* 4.2 4.0 - - + +
153D ALA* 3.8 21.7 + - + +
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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 ARG 2.7 15.9 + - - +
61A GLU* 3.6 17.5 - - + +
62A VAL 3.3 0.2 - - - -
63A ALA* 1.3 78.5 - - - +
65A LEU* 1.3 62.1 + - + +
67A ARG* 3.4 28.5 - - - +
68A LEU* 3.2 27.5 - - + +
139A ASN* 4.8 11.4 - - + +
140A CYS* 4.8 4.9 - - + +
141A ILE* 4.0 29.2 - - + -
153D ALA* 4.9 3.8 - - + +
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Residues in contact with LEU 65 (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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61A GLU 3.2 18.6 + - - +
62A VAL* 3.7 4.5 - - - +
63A ALA 3.3 0.2 - - - -
64A LEU* 1.3 77.7 - - + +
66A ARG* 1.3 66.3 + - - +
67A ARG 3.0 1.3 - - - -
68A LEU* 2.9 22.5 + - - +
69A GLU* 3.4 5.2 + - - +
79A LEU* 3.7 31.3 + - + +
96A LEU* 5.0 1.8 - - + -
98A PHE* 4.5 9.6 - - + -
141A ILE* 4.1 16.2 - - + -
164A PHE* 4.1 26.9 - - + -
165A GLY* 4.1 19.3 - - - +
166A LEU* 3.8 29.8 - - + -
169A ILE* 4.9 2.7 - - + -
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Residues in contact with ARG 66 (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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62A VAL 3.2 16.9 + - - +
63A ALA 3.8 5.2 - - - +
65A LEU* 1.3 76.3 - - - +
67A ARG* 1.3 62.0 + - - +
69A GLU* 2.4 51.3 + - - +
70A ALA 3.8 2.3 + - - -
79A LEU* 2.7 35.4 + - + -
80A MET 3.4 15.9 + - - -
82A VAL* 3.8 20.3 - - + +
37D ARG* 3.6 23.3 + - - +
149D LYS* 2.8 43.4 + - - +
150D TRP 3.8 12.6 - - - +
151D ASP* 4.1 22.9 + - - +
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Residues in contact with ARG 67 (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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63A ALA 3.1 13.5 + - - +
64A LEU* 3.4 26.6 - - - +
65A LEU 3.0 0.6 - - - -
66A ARG* 1.3 77.2 - - - +
68A LEU* 1.3 65.8 + - + +
70A ALA* 3.0 22.5 + - - +
71A PHE* 3.7 12.4 - - + -
31D LEU* 4.1 14.6 - - - +
34D LEU* 3.9 20.8 - - + +
38D TYR* 3.9 20.6 - - - +
114D ARG* 6.2 0.9 - - - +
151D ASP* 4.5 0.2 + - - -
153D ALA* 3.6 30.5 + - + +
154D ALA 5.5 1.2 + - - -
155D VAL* 4.1 20.0 - - - +
159D ASP* 5.6 2.6 + - - -
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Residues in contact with LEU 68 (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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64A LEU* 3.2 25.6 - - + +
65A LEU* 2.9 10.6 + - + +
67A ARG* 1.3 80.2 - - + +
69A GLU* 1.3 65.5 + - - +
71A PHE* 2.8 28.7 + - + +
72A GLU 3.5 2.9 + - - -
73A HIS 5.0 0.7 + - - -
76A VAL* 5.6 5.8 - - + +
135A PHE* 3.9 29.2 - - + -
136A LEU* 4.2 8.7 - - + -
139A ASN* 4.1 21.5 - - + +
141A ILE* 3.4 31.2 - - + -
164A PHE* 3.9 23.3 - - + -
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Residues in contact with GLU 69 (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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65A LEU 3.4 4.3 + - - +
66A ARG* 2.4 46.9 + - - +
67A ARG 3.2 0.6 - - - -
68A LEU* 1.3 77.5 - - - +
70A ALA* 1.3 61.3 + - - +
72A GLU* 2.9 24.7 + - - +
78A ARG* 3.2 53.7 + - + +
79A LEU 4.2 13.9 - - - +
80A MET* 4.4 4.0 - - - +
37D ARG* 2.8 26.6 + - - -
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Residues in contact with ALA 70 (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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66A ARG 3.8 1.6 + - - -
67A ARG* 3.0 17.2 + - - +
68A LEU 2.9 0.8 + - - -
69A GLU* 1.3 81.1 - - - +
71A PHE* 1.3 60.2 + - - +
72A GLU* 3.1 11.5 + - - +
34D LEU* 3.4 24.2 - - + -
37D ARG* 3.7 38.1 - - + +
38D TYR* 4.9 0.4 - - - +
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Residues in contact with PHE 71 (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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67A ARG* 3.7 21.3 - - + -
68A LEU* 2.8 24.6 + - + +
70A ALA* 1.3 77.7 - - - +
72A GLU* 1.3 68.8 + - - +
73A HIS* 3.4 1.5 + - + +
135A PHE* 3.7 31.4 - + + -
139A ASN* 4.0 20.4 - - - -
30D SER* 3.7 30.1 - - - -
33D ARG* 4.7 25.9 + - + +
34D LEU* 3.8 33.0 - - + -
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Residues in contact with GLU 72 (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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68A LEU 3.5 2.4 + - - -
69A GLU* 2.9 23.2 + - + +
70A ALA 3.8 8.1 - - - +
71A PHE* 1.3 81.1 - - - +
73A HIS* 1.3 64.6 + - - +
74A PRO* 3.6 7.3 - - - +
78A ARG* 4.2 33.5 + - - +
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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