Contacts of the strand formed by residues 74 - 97 (chain E) in PDB entry 1PPF
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 SER 74 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72E ASN* 2.7 22.9 + - - -
73E LEU* 1.3 81.4 - - - +
75E ARG* 1.3 62.6 + - - +
153E SER* 3.8 17.2 + - - -
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Residues in contact with ARG 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ASN* 3.3 39.5 + - + +
73E LEU 4.2 0.5 - - - +
74E SER* 1.3 82.5 + - - +
76E ARG* 1.3 62.0 + - - +
77E GLU* 4.4 8.3 - - + -
80E ARG* 2.9 26.3 + - - -
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Residues in contact with ARG 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B NAG 5.8 6.5 - - - +
75E ARG* 1.3 74.0 - - - +
77E GLU* 1.2 64.3 + - - +
78E PRO* 3.4 9.4 - - - +
80E ARG* 5.1 0.4 - - - +
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Residues in contact with GLU 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E HIS* 4.6 4.5 + - + -
69E GLY 4.8 1.6 - - - -
70E ALA* 3.3 3.0 - - - +
71E HIS* 2.8 33.6 + - - +
72E ASN* 2.9 33.5 + - - +
75E ARG* 3.6 9.8 + - + +
76E ARG* 1.2 78.8 - - - +
78E PRO* 1.3 69.7 - - + +
79E THR* 3.4 8.2 + - - +
80E ARG* 3.0 58.4 + - + +
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Residues in contact with PRO 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E ARG 3.4 9.2 - - - +
77E GLU* 1.3 84.6 - - + +
79E THR* 1.3 67.5 + - - +
80E ARG 3.2 6.1 + - - +
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Residues in contact with THR 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E HIS* 3.5 18.3 + - + -
69E GLY* 2.8 31.8 - - - +
77E GLU* 4.5 7.2 - - - +
78E PRO* 1.3 83.4 - - - +
80E ARG* 1.4 61.2 + - - +
81E GLN* 3.7 9.2 + - - +
115E ASN* 5.6 1.0 - - - +
117E ASN* 3.1 44.9 + - + +
118E VAL* 4.7 1.9 - - - +
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Residues in contact with ARG 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLN* 4.7 12.3 + - - +
67E VAL* 3.4 26.8 - - + +
68E LEU 3.3 12.8 - - - +
69E GLY 4.0 8.3 - - - +
70E ALA* 4.0 5.9 - - - +
72E ASN 3.1 19.6 + - - -
73E LEU* 3.6 18.2 + - - +
75E ARG 2.9 28.6 + - - -
77E GLU* 3.0 41.3 + - + +
78E PRO 3.2 7.4 - - - +
79E THR* 1.4 79.4 - - - +
81E GLN* 1.3 65.0 - - - +
82E VAL* 4.3 9.2 - - + +
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Residues in contact with GLN 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E VAL 3.6 1.1 - - - +
67E VAL* 3.5 3.6 - - - +
68E LEU* 2.8 38.1 + - + +
79E THR 4.2 6.0 + - - +
80E ARG* 1.3 79.7 - - - +
82E VAL* 1.3 61.4 + - - +
83E PHE* 3.9 19.0 - - + -
112E ALA* 3.4 9.8 - - - +
113E THR* 2.8 54.6 + - - -
115E ASN* 3.6 11.7 + - - -
118E VAL* 3.5 21.3 - - + +
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Residues in contact with VAL 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 4.0 14.4 + - - +
2B NAG 3.7 40.5 - - + +
65E ARG* 4.0 26.2 - - + -
66E VAL 3.3 8.3 - - - +
67E VAL* 4.5 19.1 - - + -
80E ARG* 4.7 9.9 - - + +
81E GLN* 1.3 79.8 - - - +
83E PHE* 1.4 74.6 + - - +
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Residues in contact with PHE 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 4.2 11.4 - - - -
65E ARG* 3.4 6.9 - - - +
66E VAL* 2.7 35.3 + - + +
68E LEU* 3.3 32.3 - - + -
81E GLN* 3.9 19.5 - - + -
82E VAL* 1.4 80.9 - - - +
84E ALA* 1.3 66.8 - - - +
108E LEU* 3.6 30.3 - - + -
109E ASN* 3.4 17.5 - - - +
110E GLY* 3.9 13.7 - - - -
111E SER 3.8 19.5 - - - -
112E ALA* 3.7 23.6 - - - -
113E THR 5.0 0.2 - - - -
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Residues in contact with ALA 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 3.4 19.2 + - - +
8B FUC 3.7 27.1 - - + -
63E ARG 5.6 1.3 - - - -
64E VAL 4.1 6.1 - - - -
66E VAL* 5.0 1.1 - - - -
83E PHE* 1.3 78.1 - - - +
85E VAL* 1.3 66.9 + - - +
108E LEU* 3.5 8.1 - - - +
109E ASN* 3.1 31.8 + - + +
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Residues in contact with VAL 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E VAL* 3.7 47.5 + - - +
64E VAL* 4.1 18.3 + - + +
66E VAL* 4.0 22.2 - - + -
84E ALA* 1.3 79.0 - - - +
86E GLN* 1.3 62.6 + - - +
87E ARG 3.5 23.8 - - - +
88E ILE* 4.1 1.1 - - + -
106E LEU* 3.9 24.9 - - + -
107E GLN 3.6 4.0 - - - +
108E LEU* 4.8 0.7 - - + +
109E ASN* 5.3 1.1 - - - -
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Residues in contact with GLN 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E ALA 3.9 0.6 + - - -
85E VAL* 1.3 74.6 - - - +
87E ARG* 1.4 62.3 + - + +
107E GLN* 2.8 36.4 + - + +
108E LEU 3.3 18.6 - - - +
109E ASN* 3.7 22.8 + - - +
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Residues in contact with ARG 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E PHE* 5.9 0.4 - - - -
85E VAL* 3.5 9.0 - - - +
86E GLN* 1.4 82.2 - - + +
88E ILE* 1.3 78.0 + - - +
89E PHE* 3.4 28.6 - - + -
106E LEU* 3.6 0.3 - - - -
107E GLN* 2.8 62.0 + - + +
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Residues in contact with ILE 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E VAL* 4.8 16.8 - - + -
63E VAL* 3.8 28.5 - - + +
85E VAL* 4.1 0.2 - - + -
87E ARG* 1.3 87.7 - - - +
89E PHE* 1.3 71.8 + - - +
90E GLU* 5.4 6.5 - - + +
104E VAL* 5.1 7.0 - - + -
105E ILE 3.4 6.5 - - - +
106E LEU* 3.2 29.4 - - + -
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Residues in contact with PHE 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E PHE* 4.0 23.3 - + - -
87E ARG* 3.4 46.4 - - + -
88E ILE* 1.3 81.9 - - - +
90E GLU* 1.3 58.7 + - - +
104E VAL* 3.5 8.7 - - - +
105E ILE* 2.9 46.4 + - + +
107E GLN* 4.0 6.3 - - + -
237E TRP* 3.7 9.2 - - + +
241E ILE* 3.7 39.3 - - + -
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Residues in contact with GLU 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E ALA* 5.2 1.1 - - + -
88E ILE* 4.3 7.8 - - + -
89E PHE* 1.3 75.1 - - - +
92E ASN* 1.3 64.2 + - - +
93E GLY* 3.1 25.1 + - - -
94E TYR* 2.8 39.8 + - + +
103E ILE 4.4 2.9 - - - +
104E VAL* 4.2 16.6 - - + -
237E TRP* 3.6 12.4 + - - -
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Residues in contact with ASN 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E GLU* 1.3 80.1 + - - +
93E GLY* 1.3 55.9 + - - +
94E TYR 3.4 1.3 - - - +
101E ASN* 2.7 39.8 + - - +
103E ILE* 4.5 8.0 + - + -
234E PHE* 3.9 18.4 - - + -
237E TRP* 3.6 48.0 - - + +
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Residues in contact with GLY 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E GLU* 3.1 16.4 + - - -
92E ASN* 1.3 76.9 - - - +
94E TYR* 1.4 67.6 - - - +
95E ASP* 3.5 6.1 + - - +
100E LEU* 4.2 0.7 - - - +
101E ASN* 3.5 14.9 + - - +
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Residues in contact with TYR 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E ALA* 3.5 28.9 - - + -
57E HIS* 3.3 33.6 - - + +
60E ALA* 4.4 14.6 - - + -
90E GLU* 2.8 21.5 + - + +
92E ASN 3.4 2.6 + - - +
93E GLY* 1.4 74.3 - - - +
95E ASP* 1.3 77.5 + - - +
96E PRO* 3.5 40.4 + - + +
99E LEU* 4.1 13.0 - - + +
100E LEU 3.4 7.9 - - - -
101E ASN 3.4 16.0 + - - +
102E ASP* 3.6 20.4 - - + -
17I THR* 5.0 0.7 - - - +
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Residues in contact with ASP 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E GLY 3.5 4.0 + - - +
94E TYR* 1.3 78.7 - - - +
96E PRO* 1.3 56.3 - - - +
97E VAL* 2.9 29.3 + - - +
98E ASN* 3.1 26.9 + - - +
99E LEU* 2.7 29.8 + - - -
100E LEU* 2.8 36.0 + - + +
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Residues in contact with PRO 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E TYR* 3.5 42.1 - - + +
95E ASP* 1.3 84.7 - - - +
97E VAL* 1.3 69.9 + - + +
99E LEU* 3.9 14.2 - - + +
13I LYS* 5.3 6.1 + - - -
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Residues in contact with VAL 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E ASP* 2.9 12.3 + - - +
96E PRO* 1.3 88.0 - - + +
98E ASN* 1.3 73.8 + - - +
99E LEU* 4.1 4.3 + - - +
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Residues in contact with ASN 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E ASP* 3.1 26.8 + - - +
97E VAL* 1.3 92.2 - - - +
99E LEU* 1.4 64.1 + - - +
100E LEU* 3.4 18.3 + - + +
177E ARG* 2.8 36.1 + - - +
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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