Contacts of the helix formed by residues 72 - 89 (chain D) in PDB entry 2FIE
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 72 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D LEU* 1.3 62.3 + - - +
74D ASP* 3.2 5.6 - - - +
75D VAL* 3.1 22.4 + - + +
76D LEU* 2.8 34.6 + - + +
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ILE* 5.2 0.7 - - + +
47D ALA* 3.7 30.7 - - + +
48D VAL* 3.9 22.9 - - + +
50D LYS* 4.1 18.6 - - - +
72D LYS* 1.3 80.2 - - - +
74D ASP* 1.3 52.6 + - - +
76D LEU* 4.5 11.2 - - + -
77D SER* 2.6 41.0 + - - +
120D LEU* 4.1 14.6 - - + -
126D ILE* 3.3 34.5 - - + -
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Residues in contact with ASP 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LYS* 3.2 2.8 - - - +
73D LEU* 1.3 74.9 - - - +
75D VAL* 1.3 69.9 + - + +
77D SER* 3.8 4.9 - - - -
78D ASN* 3.3 21.1 + - - +
98D GLU* 3.0 39.5 - - - +
119D PRO* 4.3 4.9 - - - +
120D LEU* 4.1 8.1 - - - +
123D SER* 2.9 36.8 + - - +
124D SER 4.8 0.3 + - - -
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Residues in contact with VAL 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LYS* 3.1 23.5 + - + +
74D ASP* 1.3 79.3 - - + +
76D LEU* 1.3 63.1 + - - +
78D ASN* 3.1 8.9 + - - +
79D ASP* 2.8 42.1 + - - +
98D GLU* 5.6 1.1 - - - +
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ALA* 4.2 25.4 - - + -
72D LYS* 2.8 24.0 + - + +
73D LEU* 4.1 10.5 - - + +
75D VAL* 1.3 74.9 - - - +
77D SER* 1.3 64.0 + - - +
79D ASP* 2.9 10.7 + - + +
80D LEU* 2.8 33.0 + - + +
55L HIS* 4.0 20.4 - - + +
60L ALA* 3.7 28.0 - - + -
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Residues in contact with SER 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ILE* 3.7 33.2 - - - +
73D LEU* 2.6 27.8 + - - +
74D ASP 3.8 4.7 - - - -
75D VAL 3.3 0.2 - - - -
76D LEU* 1.3 76.6 - - - +
78D ASN* 1.3 61.8 + - - +
80D LEU* 3.5 3.0 + - - +
81D VAL* 2.9 31.4 + - - +
119D PRO* 3.9 16.6 - - - -
120D LEU* 3.7 19.5 - - - +
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Residues in contact with ASN 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ASP 3.3 10.4 + - - +
75D VAL* 3.1 11.0 + - - +
77D SER* 1.3 77.2 - - - +
79D ASP* 1.3 68.1 + - - +
81D VAL* 3.8 2.0 - - - +
82D MET* 2.8 40.9 + - - +
96D SER* 2.6 32.8 + - - -
98D GLU* 3.8 18.3 - - + +
99D ASP* 3.7 17.8 + - - -
117D PHE* 3.5 8.7 - - - -
119D PRO* 3.6 8.5 - - + +
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Residues in contact with ASP 79 (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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75D VAL* 2.8 44.1 + - - +
76D LEU* 3.4 13.0 + - + +
78D ASN* 1.3 84.0 + - - +
80D LEU* 1.3 56.8 + - - +
82D MET* 3.5 4.7 - - - +
83D ASN* 2.8 34.1 + - - +
60L ALA* 3.5 21.6 - - - +
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Residues in contact with LEU 80 (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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40D ALA* 4.5 9.2 - - + -
43D ALA* 3.8 25.8 - - + +
44D ILE* 3.8 27.4 - - + +
47D ALA* 5.8 0.2 - - + -
76D LEU* 2.8 37.6 + - + +
77D SER* 3.6 4.9 - - - +
79D ASP* 1.3 78.4 - - - +
81D VAL* 1.3 57.2 + - - +
83D ASN* 3.6 0.3 - - - +
84D MET* 2.7 40.9 + - + +
55L HIS* 4.1 7.2 - - + -
59L ILE* 3.3 49.6 - - + +
60L ALA* 4.0 3.1 - - - +
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Residues in contact with VAL 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU* 4.7 14.1 - - + -
40D ALA* 4.1 13.9 - - + +
44D ILE* 3.9 20.0 - - + -
77D SER 2.9 20.4 + - - +
78D ASN 3.8 2.9 - - - +
80D LEU* 1.3 74.0 - - - +
82D MET* 1.3 62.5 + - - +
84D MET* 3.4 0.3 + - - +
85D LEU* 2.9 42.6 + - + +
117D PHE* 3.5 39.5 - - + -
119D PRO* 4.6 8.3 - - + -
134D THR* 5.0 6.1 - - + -
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Residues in contact with MET 82 (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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78D ASN* 2.8 31.0 + - - +
79D ASP* 3.5 6.5 - - - +
81D VAL* 1.3 74.0 - - - +
83D ASN* 1.3 62.5 + - - +
85D LEU* 3.8 2.0 - - - +
86D LYS* 3.1 44.4 + - - +
94D LEU* 3.3 44.7 - - + +
96D SER* 4.6 1.6 - - - -
99D ASP* 3.9 11.2 - - - +
103D ILE* 3.5 30.3 - - + -
117D PHE* 3.3 32.5 - - + -
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Residues in contact with ASN 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ASP 2.8 21.3 + - - +
80D LEU 3.7 1.3 - - - +
82D MET* 1.3 72.1 - - - +
84D MET* 1.3 64.7 + - - +
86D LYS* 3.7 9.1 + - - +
87D SER* 3.0 27.6 + - - -
9H ASP* 5.5 2.1 - - - +
10H VAL* 3.8 10.7 - - - +
58L GLY 2.5 31.1 + - - +
59L ILE* 3.2 15.4 + - - +
60L ALA 4.4 7.0 - - - +
61L GLY* 4.1 11.7 - - - -
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Residues in contact with MET 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D SER* 3.6 25.5 + - - +
39D THR* 3.9 25.1 - - + +
40D ALA* 4.3 17.3 - - + -
80D LEU* 2.7 25.7 + - + +
81D VAL 4.0 2.7 - - - +
83D ASN* 1.3 70.1 - - - +
85D LEU* 1.3 64.8 + - + +
87D SER* 3.3 2.1 + - - -
88D SER 3.1 16.3 + - - -
10H VAL* 4.1 19.3 - - + -
12H THR* 5.1 7.9 - - + -
15H ARG* 3.4 35.4 + - - +
59L ILE* 3.9 33.2 - - + +
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Residues in contact with LEU 85 (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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33D LEU* 3.6 45.1 - - + +
36D SER* 4.8 3.1 - - - -
37D LEU* 4.8 12.1 - - + +
81D VAL* 2.9 28.2 + - + +
82D MET 3.8 3.4 - - - +
84D MET* 1.3 74.9 - - + +
86D LYS* 1.3 66.3 + - - +
88D SER* 2.8 25.9 + - - -
91D THR* 3.6 11.0 + - + -
94D LEU* 3.5 33.0 - - + -
115D VAL* 3.7 19.7 - - + -
117D PHE* 3.9 15.3 - - + -
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Residues in contact with LYS 86 (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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82D MET* 3.1 34.8 + - - +
83D ASN* 3.9 9.0 - - - +
85D LEU* 1.3 79.6 - - - +
87D SER* 1.3 62.2 + - - +
88D SER 3.2 1.2 + - - -
89D PHE 3.4 8.7 + - - -
91D THR* 4.2 6.7 + - - -
94D LEU* 4.4 10.1 - - + -
103D ILE* 4.3 25.9 - - - +
105D VAL* 4.2 22.0 - - + +
106D GLU* 4.4 14.9 - - - +
109D LYS* 3.5 30.7 - - + +
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Residues in contact with SER 87 (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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83D ASN* 3.0 21.1 + - - -
84D MET* 3.4 2.0 - - - -
85D LEU 3.1 0.6 - - - -
86D LYS* 1.3 76.9 - - - +
88D SER* 1.3 62.9 - - - +
89D PHE* 3.0 17.1 - - - -
109D LYS* 5.1 0.2 - - - -
9H ASP* 2.9 29.3 + - - -
10H VAL* 4.0 8.8 - - - +
15H ARG* 3.1 43.8 + - - -
19H GLU* 4.7 0.7 - - - +
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Residues in contact with SER 88 (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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32D GLN* 3.7 28.4 + - - +
33D LEU* 3.6 11.0 - - - +
36D SER* 3.1 31.2 - - - -
84D MET 3.1 4.0 + - - -
85D LEU 2.8 17.4 + - - -
87D SER* 1.3 76.0 - - - +
89D PHE* 1.3 68.5 + - - +
90D ALA* 2.8 31.5 + - - +
15H ARG* 3.8 4.0 - - - +
19H GLU* 4.7 1.2 - - - +
22H ARG* 4.7 0.2 + - - -
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Residues in contact with PHE 89 (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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29D GLU* 3.7 7.9 - - - +
32D GLN* 5.2 2.5 - - - +
85D LEU 3.9 0.2 + - - -
86D LYS 3.4 7.2 + - - -
87D SER* 3.0 29.9 - - - -
88D SER* 1.3 79.5 + - - +
90D ALA* 1.3 57.7 + - - +
108D GLU 3.1 28.0 - - - -
109D LYS* 3.2 49.1 - - + -
110D ARG 3.4 7.1 - - - +
111D GLY* 3.3 11.7 - - - -
9H ASP* 4.6 4.9 - - + -
19H GLU* 4.6 13.0 - - - +
22H ARG* 5.5 1.2 + - - +
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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
------------------------------------------------------------
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