Contacts of the helix formed by residues 51 - 71 (chain S) in PDB entry 1PP9
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 51 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ARG* 3.5 27.3 - - - +
3010B PO4 4.5 11.0 - - - +
50S LEU* 1.3 88.2 - - + +
52S GLU* 1.3 66.8 + - - +
53S ASN* 3.3 16.4 - - - +
54S LEU* 3.1 23.2 + - + -
55S TYR* 3.1 17.5 + - - +
93S TYR* 3.2 28.3 - - + +
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Residues in contact with GLU 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50S LEU 3.8 1.6 + - - -
51S PRO* 1.3 70.4 - - - +
53S ASN* 1.3 58.0 + - - +
55S TYR* 3.3 6.1 + - - +
56S ASP* 2.8 65.0 + - - +
9T ARG* 3.1 31.9 + - - -
11T ARG* 3.2 24.2 + - - -
12T HIS* 4.7 1.4 + - - -
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Residues in contact with ASN 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51S PRO* 3.7 20.1 - - - +
52S GLU* 1.3 75.8 - - - +
54S LEU* 1.3 76.6 + - - +
56S ASP* 4.0 4.0 - - - -
57S ASP* 3.0 43.3 + - - +
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Residues in contact with LEU 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S LEU* 4.3 18.3 - - + +
51S PRO* 3.1 34.8 + - + +
53S ASN* 1.3 94.3 - - - +
55S TYR* 1.3 61.2 + - - +
57S ASP* 3.6 9.9 + - + +
58S ARG* 3.1 24.8 + - - +
61S ARG* 5.0 1.0 + - - -
89S TYR* 4.2 38.6 - - + +
93S TYR* 4.4 6.7 - - + +
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Residues in contact with TYR 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215P VAL* 5.5 0.2 - - - +
47S ILE* 3.9 38.1 - - + -
48S ARG* 5.7 1.8 - - - -
50S LEU* 4.2 19.8 - - + +
51S PRO 3.1 11.9 + - - +
52S GLU* 3.6 10.5 - - - +
54S LEU* 1.3 78.0 - - - +
56S ASP* 1.3 73.8 + - - +
58S ARG* 3.3 5.1 + - - +
59S VAL* 3.0 48.8 + - + +
8T THR* 3.4 16.8 + - - -
9T ARG* 2.8 48.4 + - + +
10T VAL* 5.3 0.9 - - - -
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Residues in contact with ASP 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237Q TYR* 3.1 29.6 + - + +
239Q PRO* 5.6 0.7 - - + -
240Q PRO* 5.6 0.3 - - - +
52S GLU* 2.8 48.4 + - - +
53S ASN* 4.1 3.6 - - - +
55S TYR* 1.3 85.9 - - - +
57S ASP* 1.3 64.5 + - - +
59S VAL* 3.3 6.6 + - - +
60S PHE* 3.0 18.7 + - - +
9T ARG* 5.4 0.5 + - - -
11T ARG* 3.8 22.3 + - - +
12T HIS* 3.8 21.7 + - + -
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Residues in contact with ASP 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237Q TYR* 2.7 39.2 + - - -
239Q PRO* 5.3 2.1 - - - +
53S ASN* 3.0 31.4 + - - +
54S LEU* 3.9 11.6 - - + +
56S ASP* 1.3 72.8 - - - +
58S ARG* 1.3 66.9 + - - +
60S PHE* 3.2 2.9 + - - +
61S ARG* 2.9 46.7 + - - +
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Residues in contact with ARG 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211P ILE* 5.5 0.6 - - - +
34S ASP 2.8 27.7 + - - -
35S ASP* 3.8 10.1 + - - +
37S ILE* 4.0 15.4 + - - +
39S GLU* 4.0 11.7 + - - +
47S ILE* 3.5 40.4 - - - +
50S LEU* 4.5 13.7 - - - -
54S LEU 3.1 19.0 + - - +
55S TYR* 3.5 7.0 - - - +
57S ASP* 1.3 77.9 - - - +
59S VAL* 1.3 66.0 + - - +
61S ARG* 3.3 15.4 + - - +
62S ILE* 3.0 52.0 + - + +
89S TYR* 2.8 27.2 + - + +
90S LEU* 4.5 4.4 - - - +
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Residues in contact with VAL 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215P VAL* 3.9 29.9 - - + +
55S TYR* 3.0 50.8 + - + +
56S ASP* 3.5 10.1 - - - +
58S ARG* 1.3 79.5 - - + +
60S PHE* 1.3 59.8 + - - +
62S ILE* 3.4 4.9 + - - +
63S LYS* 2.9 29.8 + - + +
9T ARG 3.9 4.3 - - - +
10T VAL* 4.1 26.9 - - + -
11T ARG 5.3 2.5 - - - +
13T VAL* 4.9 5.2 - - + -
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Residues in contact with PHE 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235Q LEU* 4.2 27.4 - - + -
236Q ALA* 4.2 7.0 - - - -
237Q TYR* 3.5 59.9 - + + -
56S ASP 3.0 12.1 + - - +
57S ASP 3.2 6.0 + - - +
59S VAL* 1.3 80.4 - - - +
61S ARG* 1.3 60.8 + - + +
63S LYS* 3.2 5.9 + - + +
64S ARG* 2.8 66.4 + - + +
13T VAL* 4.1 20.6 - - + -
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Residues in contact with ARG 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S LEU 4.7 2.1 - - - +
30S GLY 3.6 19.0 - - - +
31S LEU* 3.7 4.1 - - + +
32S MET* 3.6 24.8 - - - +
35S ASP* 2.8 46.2 + - - +
54S LEU 5.0 1.0 + - - -
57S ASP* 2.9 40.1 + - - +
58S ARG* 3.7 12.7 - - - +
60S PHE* 1.3 79.3 - - + +
62S ILE* 1.3 58.7 + - - +
64S ARG* 3.3 23.3 + - - +
65S ALA* 2.9 28.9 + - - +
89S TYR* 3.2 25.1 - - - -
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Residues in contact with ILE 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211P ILE* 3.8 32.1 - - + -
212P SER* 3.8 7.2 - - - +
215P VAL* 3.9 11.0 - - + -
31S LEU* 4.1 7.4 - - + -
35S ASP* 4.2 17.3 - - + +
39S GLU* 5.8 0.7 - - - +
58S ARG* 3.0 56.3 + - + +
59S VAL* 3.8 5.4 - - - +
61S ARG* 1.3 74.8 - - - +
63S LYS* 1.3 58.5 + - - +
65S ALA* 3.1 2.5 + - - +
66S LEU* 2.8 49.3 + - + +
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Residues in contact with LYS 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215P VAL* 3.5 33.4 + - + +
216P ASP* 3.3 28.6 + - + +
233Q ARG* 4.2 6.7 - - - +
235Q LEU* 4.1 24.5 - - + +
59S VAL* 2.9 18.2 + - + +
60S PHE* 3.7 8.3 - - + +
62S ILE* 1.3 76.3 - - - +
64S ARG* 1.3 63.4 + - - +
66S LEU* 3.3 6.6 + - - +
67S ASP* 3.0 24.1 + - - +
10T VAL* 5.2 7.4 - - + -
13T VAL* 3.8 35.7 - - + -
15T THR* 4.4 5.8 + - - -
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Residues in contact with ARG 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235Q LEU* 4.6 7.6 - - + +
29S LEU 4.1 7.7 + - - -
30S GLY* 3.2 32.3 + - - -
60S PHE* 2.8 50.5 + - + +
61S ARG* 3.7 20.0 + - - +
63S LYS* 1.3 74.3 - - - +
65S ALA* 1.3 61.6 + - - +
67S ASP* 3.4 7.8 + - - +
68S LEU* 3.1 31.9 + - + +
75S LEU* 4.3 22.2 - - + +
79S GLN* 4.5 16.5 + - - +
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Residues in contact with ALA 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209P THR* 5.5 2.9 - - + -
211P ILE* 5.8 1.1 - - + -
29S LEU* 3.9 24.9 + - + +
31S LEU* 3.5 35.4 - - + -
61S ARG 2.9 16.8 + - - +
62S ILE* 3.6 3.8 - - - +
64S ARG* 1.3 75.2 - - - +
66S LEU* 1.3 66.8 + - + +
68S LEU* 3.3 4.0 + - - +
69S SER* 2.9 24.5 + - - -
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Residues in contact with LEU 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P SER* 4.1 3.8 + - - +
26P ASN* 3.6 31.4 - - - +
207P ASN* 3.8 7.6 - - - +
209P THR* 3.8 21.3 - - + +
211P ILE* 4.7 3.1 - - + +
212P SER 3.9 0.4 - - - +
213P SER* 3.8 25.6 - - - -
215P VAL* 4.1 4.5 - - + -
216P ASP* 3.8 29.2 - - + +
62S ILE* 2.8 41.4 + - + +
63S LYS 3.8 4.0 - - - +
65S ALA* 1.3 72.4 - - + +
67S ASP* 1.3 57.1 + - - +
69S SER* 3.3 4.9 + - - -
70S MET* 3.0 28.9 + - - +
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Residues in contact with ASP 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216P ASP* 4.3 0.6 + - - -
230Q LEU 4.5 0.2 - - - +
233Q ARG* 3.0 49.1 + - - +
235Q LEU* 3.9 19.7 - - + +
63S LYS 3.0 17.5 + - - +
64S ARG* 3.5 6.6 - - - +
66S LEU* 1.3 74.7 - - - +
68S LEU* 1.3 64.3 + - - +
70S MET* 3.3 14.3 + - - +
71S ARG* 3.1 49.5 + - - +
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Residues in contact with LEU 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S LEU* 3.6 33.0 - - + +
64S ARG* 3.1 21.5 + - + +
65S ALA 3.3 5.6 + - - +
67S ASP* 1.3 76.1 - - - +
69S SER* 1.3 57.7 + - - +
71S ARG* 3.1 27.8 + - - +
72S GLN 2.9 8.0 + - - -
73S GLN* 2.9 43.0 + - + +
74S ILE 3.8 23.1 - - - +
75S LEU* 3.6 35.7 - - + +
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Residues in contact with SER 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P ASN* 2.9 31.2 + - - +
208P PRO* 4.4 7.8 - - - +
209P THR* 4.1 14.8 - - - +
316P MET* 4.6 5.1 - - - +
29S LEU* 4.8 8.4 - - - +
65S ALA 2.9 17.1 + - - -
66S LEU 3.5 5.2 - - - -
68S LEU* 1.3 78.8 - - - +
70S MET* 1.3 60.9 + - - +
72S GLN* 3.1 27.0 + - - +
73S GLN 4.9 1.6 - - - -
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Residues in contact with MET 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P SER* 3.2 37.5 - - - +
26P ASN* 3.6 11.0 - - + +
227Q TRP* 4.0 15.5 - - + -
230Q LEU* 3.4 46.9 - - - +
231Q LYS* 3.5 18.3 - - + -
233Q ARG* 4.4 7.2 - - - +
3003Q CDL 3.5 9.5 + - - -
66S LEU 3.0 16.2 + - - +
67S ASP* 3.6 13.9 - - - +
68S LEU 3.2 0.6 - - - -
69S SER* 1.3 76.4 - - - +
71S ARG* 1.3 82.1 + - + +
72S GLN* 3.2 0.9 - - - +
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Residues in contact with ARG 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231Q LYS* 3.3 39.9 - - + +
233Q ARG 5.3 3.2 + - - -
3003Q CDL 3.6 12.8 - - - +
13R TYR* 5.8 1.1 - - - -
67S ASP* 3.1 32.9 + - - +
68S LEU* 3.1 31.6 + - - +
70S MET* 1.3 98.5 - - + +
72S GLN* 1.3 71.4 + - - +
73S GLN* 3.0 65.9 + - - +
36T ASN* 4.2 1.0 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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