Contacts of the helix formed by residues 45 - 66 (chain U) in PDB entry 1P7G
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 LYS 45 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41U LEU* 3.0 28.3 + - + +
44U GLN* 1.3 98.0 + - + +
46U HIS* 1.3 56.5 + - - +
48U GLN* 3.4 1.4 + - - +
49U GLY* 2.7 33.8 + - - -
188W ASN* 3.5 43.3 - - + +
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Residues in contact with HIS 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41U LEU 3.3 22.1 + - - -
42U HIS* 3.4 26.5 - - + +
45U LYS* 1.3 74.8 - - - +
47U HIS* 1.3 67.0 + - - +
49U GLY* 3.1 10.3 + - - -
50U TYR* 3.1 27.3 + - + -
180U HIS* 3.0 44.8 + + + +
179W GLU* 4.0 2.9 - - - -
183W TYR* 2.6 32.5 + + - -
188W ASN* 3.4 27.7 - - + +
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Residues in contact with HIS 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20U LEU* 3.4 11.8 - - + +
21U PRO* 3.6 23.5 - - + +
42U HIS 2.9 17.9 + - - +
43U HIS* 3.4 15.1 - - - +
46U HIS* 1.3 70.9 - - - +
48U GLN* 1.3 64.3 + - - +
50U TYR* 2.9 20.8 + + - +
51U VAL* 3.2 7.0 + - + +
86U GLY 4.5 0.7 - - - -
87U HIS* 3.0 40.5 + - - -
90U HIS* 3.4 28.0 - + + +
91U SER* 3.7 9.4 - - - -
94U TRP* 2.8 30.5 + - + -
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Residues in contact with GLN 48 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20U LEU* 3.3 38.9 - - + +
43U HIS 3.2 6.2 + - - +
44U GLN* 2.8 28.9 - - - +
45U LYS 3.6 1.6 - - - +
46U HIS 3.3 0.4 - - - -
47U HIS* 1.3 78.3 - - - +
49U GLY* 1.3 63.5 + - - +
51U VAL* 3.1 11.8 + - - +
52U ASN* 2.9 57.7 + - - +
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Residues in contact with GLY 49 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45U LYS 2.7 21.6 + - - -
46U HIS 3.1 4.0 + - - -
48U GLN* 1.3 72.6 - - - +
50U TYR* 1.3 61.3 + - - +
52U ASN* 3.6 11.1 - - - +
53U GLY* 2.8 23.9 + - - -
83U HIS* 3.6 6.6 + - - -
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Residues in contact with TYR 50 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46U HIS* 3.1 30.6 + - + +
47U HIS* 2.9 14.1 + - - +
49U GLY* 1.3 74.6 - - - +
51U VAL* 1.3 67.6 + - - +
54U ALA* 2.8 25.6 + - - +
82U PHE* 3.8 12.8 - + - -
83U HIS* 3.3 38.7 - + - +
86U GLY* 4.0 11.0 - - - -
87U HIS* 3.9 7.6 - - - +
90U HIS* 3.5 31.2 - + - -
161U HIS* 3.1 27.1 + + - -
178U TRP* 4.1 6.3 - + - -
180U HIS* 3.2 26.2 - - - -
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Residues in contact with VAL 51 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18U TYR* 3.2 37.2 - - + +
19U THR* 3.6 14.8 - - - +
20U LEU* 3.9 10.5 - - + +
47U HIS* 3.2 14.6 + - + +
48U GLN* 3.1 12.5 + - - +
50U TYR* 1.3 76.4 - - - +
52U ASN* 1.3 61.4 + - - +
54U ALA* 3.2 6.9 + - - +
55U ASN* 2.9 32.2 + - - +
87U HIS* 3.3 37.2 - - + +
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Residues in contact with ASN 52 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48U GLN* 2.9 48.1 + - - +
49U GLY* 3.6 11.4 - - - +
51U VAL* 1.3 76.1 - - - +
53U GLY* 1.3 59.9 + - - +
55U ASN* 3.1 10.3 + - - +
56U ALA* 2.8 30.5 + - - +
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Residues in contact with GLY 53 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49U GLY 2.8 15.9 + - - -
52U ASN* 1.3 72.1 - - - +
54U ALA* 1.3 61.6 + - - +
56U ALA* 3.3 8.7 + - - +
57U ALA* 3.2 22.9 + - - +
79U ASP* 5.4 1.0 - - - +
83U HIS* 3.4 36.8 + - - -
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Residues in contact with ALA 54 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18U TYR* 4.1 20.9 - - + -
50U TYR 2.8 18.1 + - - +
51U VAL* 3.3 7.9 - - - +
53U GLY* 1.3 77.0 - - - +
55U ASN* 1.3 62.6 + - - +
57U ALA* 3.3 5.8 + - - +
58U LEU* 3.2 25.7 + - - +
80U LEU* 3.9 9.0 - - + +
83U HIS* 3.3 13.1 - - + +
84U LEU* 4.0 17.5 - - + +
87U HIS* 5.3 1.6 - - + -
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Residues in contact with ASN 55 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17U ARG* 3.5 26.5 + - - +
18U TYR* 2.7 52.4 + - - +
51U VAL* 2.9 25.6 + - - +
52U ASN* 3.6 8.7 + - - +
54U ALA* 1.3 73.4 - - - +
56U ALA* 1.3 66.4 + - - +
58U LEU* 3.2 7.9 + - - +
59U GLU* 3.0 22.5 + - - +
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Residues in contact with ALA 56 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52U ASN 2.8 20.2 + - - +
53U GLY* 3.6 9.9 - - - +
55U ASN* 1.3 72.1 - - - +
57U ALA* 1.3 63.7 + - - +
59U GLU* 3.3 15.7 + - - +
60U LYS* 3.3 29.1 + - - +
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Residues in contact with ALA 57 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53U GLY 3.2 10.8 + - - +
54U ALA 3.6 8.1 - - - +
55U ASN 3.2 0.2 - - - -
56U ALA* 1.3 78.4 - - - +
58U LEU* 1.3 65.0 + - - +
60U LYS* 3.2 10.8 + - - +
61U LEU* 3.1 20.7 + - - +
76U VAL* 3.5 21.9 - - + +
79U ASP* 4.5 5.6 - - + -
80U LEU* 3.8 35.9 - - + +
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Residues in contact with LEU 58 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U THR* 4.2 15.8 - - + +
16U LYS 3.1 27.8 - - - +
17U ARG* 3.4 24.9 - - - +
18U TYR* 3.6 21.1 - - + -
54U ALA 3.2 16.7 + - - +
55U ASN* 3.2 7.4 + - - +
57U ALA* 1.3 73.6 - - - +
59U GLU* 1.3 57.0 + - - +
61U LEU* 3.1 10.3 + - + +
62U GLU* 2.7 37.2 + - - +
65U ARG* 5.7 0.9 - - - +
80U LEU* 4.2 12.8 - - + -
152X GLN* 4.4 4.5 - - - +
154X LEU* 4.0 27.4 - - + -
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Residues in contact with GLU 59 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17U ARG* 3.2 29.5 + - - +
55U ASN 3.0 12.9 + - - +
56U ALA* 3.5 12.8 - - - +
57U ALA 3.2 0.4 - - - -
58U LEU* 1.3 77.1 - - - +
60U LYS* 1.3 61.0 + - + +
62U GLU* 3.9 8.9 - - - +
63U LYS* 3.1 64.8 + - + +
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Residues in contact with LYS 60 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56U ALA* 3.4 24.3 - - - +
57U ALA* 3.2 8.1 + - - +
58U LEU 3.1 0.8 - - - -
59U GLU* 1.3 77.6 - - + +
61U LEU* 1.3 64.7 + - - +
63U LYS* 3.6 6.9 + - - +
64U PHE* 3.1 22.5 + - - +
69U ALA* 5.6 0.5 - - - +
70U GLN 4.8 2.1 - - - +
71U ILE* 3.8 6.7 - - + +
76U VAL* 4.1 30.7 - - + +
79U ASP* 4.3 15.3 + - - +
72V ASP* 6.1 3.2 - - - -
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Residues in contact with LEU 61 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57U ALA 3.1 19.3 + - - +
58U LEU* 3.1 14.1 + - + +
60U LYS* 1.3 73.9 - - - +
62U GLU* 1.3 55.0 + - - +
64U PHE* 3.1 3.2 + - + +
65U ARG* 2.7 63.7 + - - +
71U ILE* 3.4 22.0 - - + -
73U ILE* 4.2 3.1 - - + -
76U VAL* 3.9 7.6 - - + -
77U LEU* 4.1 20.2 - - + -
80U LEU* 3.8 28.9 - - + -
128X GLU* 3.4 27.8 - - - +
154X LEU* 5.5 0.2 - - + -
155X ILE 5.7 0.7 - - - +
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Residues in contact with GLU 62 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13U VAL* 4.4 3.1 - - + -
14U THR* 4.2 1.2 - - - -
15U THR* 2.7 43.9 + - + +
17U ARG* 3.3 17.0 + - - +
58U LEU 2.7 21.1 + - - +
59U GLU* 3.9 13.0 - - - +
61U LEU* 1.3 72.9 - - - +
63U LYS* 1.3 63.6 + - + +
65U ARG* 3.2 13.1 + - - +
66U LYS* 3.0 60.7 + - + +
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Residues in contact with LYS 63 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59U GLU* 3.1 41.7 + - + +
60U LYS* 3.8 7.0 - - - +
61U LEU 3.3 0.2 - - - -
62U GLU* 1.3 80.4 - - + +
64U PHE* 1.3 63.5 + - - +
66U LYS* 3.1 8.2 + - - +
68U GLU* 3.0 60.3 + - + +
69U ALA* 3.1 30.8 + - + +
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Residues in contact with PHE 64 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60U LYS 3.1 12.3 + - - +
61U LEU 3.1 7.7 + - - +
63U LYS* 1.3 72.8 - - - +
65U ARG* 1.3 56.1 + - + +
66U LYS 3.0 8.8 + - - -
67U GLY* 3.0 8.7 + - - -
69U ALA* 3.3 23.6 - - - +
70U GLN* 4.1 4.5 - - - +
71U ILE* 3.5 41.7 - - + -
124X LYS* 2.8 37.6 + - + -
127X GLU* 3.4 42.0 - - + -
128X GLU* 3.5 47.3 - - + -
131X GLN* 5.4 5.8 - - + -
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Residues in contact with ARG 65 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13U VAL* 3.3 29.3 - - + +
14U THR 4.4 0.2 + - - -
15U THR* 3.7 20.4 - - - +
58U LEU* 5.7 0.8 - - - +
61U LEU* 2.7 47.0 + - - +
62U GLU* 3.5 5.8 - - - +
64U PHE* 1.3 72.2 - - + +
66U LYS* 1.3 57.9 + - - +
67U GLY 3.4 1.1 - - - -
118X PHE* 3.1 32.8 + - - +
119X PHE* 3.4 23.8 - - + +
120X GLY* 5.3 0.3 - - - -
124X LYS* 3.7 32.5 - - + +
128X GLU* 2.9 41.9 + - - +
152X GLN* 5.4 1.4 + - - -
153X LEU 4.7 8.7 + - - -
154X LEU* 4.9 6.7 - - - +
155X ILE 4.8 5.7 - - - +
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Residues in contact with LYS 66 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12U SER* 5.7 0.4 - - - +
13U VAL* 3.0 49.0 + - + +
62U GLU* 3.0 44.3 + - + +
63U LYS* 3.7 3.4 - - - +
64U PHE 3.0 1.2 - - - -
65U ARG* 1.3 81.1 - - - +
67U GLY* 1.3 56.9 + - - +
68U GLU* 2.8 42.1 + - - +
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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