Contacts of the helix formed by residues 63 - 76 (chain D) in PDB entry 1P7L
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 ASP 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B TRP* 4.5 9.6 - - + -
97B LYS* 2.7 33.0 + - - -
62D VAL* 1.3 74.4 - - - +
64D ILE* 1.3 64.8 + - - +
65D GLU* 3.2 16.3 + - - +
66D GLU* 3.5 22.1 + - + +
67D ILE* 3.0 31.3 + - + +
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Residues in contact with ILE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D VAL* 4.2 23.1 - - + -
30D ILE* 6.0 0.2 - - + -
52D VAL* 3.7 28.9 - - + -
56D ILE* 5.8 0.9 - - + -
62D VAL* 3.9 25.3 + - + +
63D ASP* 1.3 70.8 + - - +
65D GLU* 1.3 58.8 + - - +
67D ILE* 4.0 4.2 - - + +
68D THR* 2.5 48.4 + - - +
91D VAL* 4.6 3.8 - - + -
93D SER* 3.7 20.4 - - - +
95D ILE* 4.2 20.4 - - + -
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A THR* 5.9 0.2 - - - +
95B ILE 4.0 9.4 - - - +
96B GLY* 3.3 29.3 - - - -
97B LYS* 4.0 14.7 + - - +
63D ASP* 3.2 8.5 + - - +
64D ILE* 1.3 78.1 - - - +
66D GLU* 1.3 71.9 + - - +
68D THR* 3.5 0.3 - - - -
69D ARG* 2.5 81.1 + - - +
91D VAL* 3.9 21.5 - - + +
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Residues in contact with GLU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LYS* 2.7 34.3 + - - +
63D ASP* 3.5 21.7 + - + +
64D ILE 3.3 0.4 - - - -
65D GLU* 1.3 89.0 - - - +
67D ILE* 1.3 66.0 + - + +
69D ARG* 4.6 8.2 - - - +
70D ASN* 3.0 45.4 + - - +
73D ARG* 5.7 1.0 + - - -
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Residues in contact with ILE 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 4.9 1.1 - - + +
25D ALA* 3.7 36.1 - - + +
26D VAL* 4.0 15.5 - - + +
29D ALA* 3.4 30.7 - - + -
62D VAL* 4.0 15.5 - - + -
63D ASP* 3.0 31.0 + - + +
64D ILE* 4.0 4.9 - - - +
66D GLU* 1.3 76.6 - - + +
68D THR* 1.3 55.7 + - - +
70D ASN* 3.9 4.2 - - - +
71D THR* 2.6 38.4 + - - +
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Residues in contact with THR 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.5 32.8 - - + +
26D VAL* 5.2 0.3 - - - +
50D VAL* 3.5 24.5 - - + -
52D VAL* 3.9 6.1 - - - +
64D ILE* 2.5 35.6 + - - +
65D GLU 3.5 2.7 - - - -
67D ILE* 1.3 76.9 - - - +
69D ARG* 1.3 69.4 + - - +
71D THR* 2.8 17.4 + - - -
72D VAL* 2.8 15.1 + - + +
89D CYS* 5.9 1.6 - - - -
91D VAL* 4.0 14.7 - - + +
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Residues in contact with ARG 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A THR* 3.8 21.6 + - - +
65D GLU* 2.5 63.5 + - + +
66D GLU* 4.2 9.2 - - - +
68D THR* 1.3 71.9 - - - +
70D ASN* 1.3 52.8 + - - +
72D VAL* 4.8 1.6 - - - -
73D ARG* 2.8 47.7 + - - +
86D ALA* 2.8 50.3 + - - +
87D ASN* 3.7 15.3 + - - +
89D CYS* 2.4 48.5 + - - +
91D VAL* 3.5 18.4 - - + +
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Residues in contact with ASN 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D GLU* 3.0 40.2 + - - +
67D ILE* 3.9 4.1 - - - +
69D ARG* 1.3 77.5 - - - +
71D THR* 1.3 62.8 + - - +
73D ARG* 2.6 35.7 + - - +
74D GLU* 3.0 40.3 + - - +
352D LYS* 5.4 0.4 - - - +
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Residues in contact with THR 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D GLN* 4.0 17.0 - - + +
22D ILE* 4.0 31.6 - - + +
25D ALA* 3.3 13.5 - - + +
67D ILE* 2.6 25.2 + - - +
68D THR* 2.8 13.2 + - - -
70D ASN* 1.3 74.2 - - - +
72D VAL* 1.3 62.3 + - - +
74D GLU* 3.5 4.8 + - - +
75D ILE* 3.2 22.8 + - + +
352D LYS* 3.2 29.3 + - - +
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Residues in contact with VAL 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 4.0 28.3 - - + -
22D ILE* 4.1 14.6 - - + -
50D VAL* 4.8 3.4 - - + -
68D THR* 2.8 15.5 + - + +
69D ARG* 3.8 2.7 - - - +
71D THR* 1.3 70.3 - - - +
73D ARG* 1.3 72.4 + - - +
75D ILE* 2.7 27.4 + - + +
76D GLY 3.0 4.2 + - - -
77D TYR* 3.8 14.7 + - + +
84D PHE* 4.2 25.8 - - + -
86D ALA* 3.2 30.7 - - + +
89D CYS* 5.7 1.6 - - - -
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Residues in contact with ARG 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D GLU* 5.7 1.2 + - - -
69D ARG* 2.8 37.2 + - - +
70D ASN* 2.6 44.4 + - - +
72D VAL* 1.3 71.4 - - - +
74D GLU* 1.3 65.9 + - - +
76D GLY* 2.9 18.2 + - - -
77D TYR 4.5 0.2 - - - -
78D VAL* 3.9 23.8 - - + +
86D ALA* 3.5 9.6 - - + +
87D ASN* 3.1 41.0 + - - +
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Residues in contact with GLU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLU* 4.9 0.9 - - - -
70D ASN* 3.0 35.2 + - - +
71D THR* 3.8 4.7 - - - +
73D ARG* 1.3 76.0 - - - +
75D ILE* 1.3 67.8 + - - +
76D GLY* 3.3 1.2 + - - -
153D LYS* 3.8 16.6 + - - -
352D LYS* 3.8 21.5 + - - +
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Residues in contact with ILE 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLU* 3.6 36.1 - - - +
13D GLY* 3.9 14.4 - - - -
18D ILE* 4.0 28.0 - - + -
21D GLN* 3.8 25.6 - - + +
71D THR* 3.2 28.3 + - + +
72D VAL* 2.7 24.4 + - + +
74D GLU* 1.3 75.2 - - - +
76D GLY* 1.3 57.0 + - - +
77D TYR* 4.1 18.4 - - + -
152D ARG* 2.9 25.8 + - - -
153D LYS* 5.7 0.2 - - - +
162D PRO* 4.3 1.7 - - + +
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Residues in contact with GLY 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D VAL 3.0 1.8 + - - -
73D ARG 2.9 14.7 + - - -
74D GLU 4.2 0.9 - - - -
75D ILE* 1.3 80.0 - - - +
77D TYR* 1.3 60.1 + - - +
78D VAL* 3.0 19.6 + - - +
82D MET* 3.4 12.1 - - - +
152D ARG* 4.6 3.1 - - - -
162D PRO* 3.8 14.6 - - - -
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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