Contacts of the helix formed by residues 79 - 95 (chain B) in PDB entry 2FI2
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 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 3.9 13.7 - - - +
77B VAL 4.1 0.8 + - - -
78B ARG* 1.3 79.3 - - - +
80B LYS* 1.3 66.2 + - - +
81B GLU* 2.5 28.8 + - - -
82B GLN* 3.2 19.8 + - - +
83B MET* 3.3 15.1 + - - +
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Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PRO* 3.5 33.7 + - + +
77A VAL 5.6 0.6 - - - -
78A ARG 2.9 29.8 + - - +
79A SER* 3.7 18.5 - - - +
80A LYS* 3.7 26.5 - - + +
83A MET* 3.6 20.7 - - + +
79B SER* 1.3 76.3 - - - +
81B GLU* 1.3 60.0 + - - +
83B MET* 3.1 9.3 + - - +
84B LEU* 3.0 27.8 + - - +
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO* 4.6 6.4 - - + +
79B SER* 2.5 34.3 + - - -
80B LYS* 1.3 79.1 + - - +
82B GLN* 1.3 84.5 + - - +
84B LEU* 3.1 35.3 - - + +
85B GLU* 3.3 13.9 + - - +
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Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 4.2 26.4 + - + +
79B SER* 3.5 18.2 - - - +
81B GLU* 1.3 100.2 + - - +
83B MET* 1.3 64.0 - - - +
85B GLU* 3.3 19.5 + - - +
86B LEU* 3.2 28.1 + - - +
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Residues in contact with MET 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 4.9 3.1 - - + -
80A LYS* 3.8 30.5 - - + +
83A MET* 4.0 23.8 - - + +
87A LEU* 6.0 0.4 - - + -
73B LEU* 3.8 44.1 - - + +
75B PRO* 3.6 29.6 - - + -
78B ARG* 3.6 26.2 - - + +
79B SER 3.4 9.0 - - - +
80B LYS* 3.1 7.8 + - - +
82B GLN* 1.3 75.7 - - - +
84B LEU* 1.3 64.8 + - - +
86B LEU* 3.4 4.8 + - + +
87B LEU* 3.0 26.3 + - - +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ARG* 4.9 5.2 - - + +
69A CYS* 4.1 6.9 - - - -
70A ARG* 3.7 38.8 - - + +
73A LEU* 3.5 35.7 - - + -
75A PRO* 3.9 22.7 - - + -
83A MET* 5.2 0.2 - - + -
80B LYS 3.0 17.6 + - - +
81B GLU* 3.1 23.6 - - + +
83B MET* 1.3 75.6 - - - +
85B GLU* 1.3 58.2 + - - +
87B LEU* 3.0 4.3 + - - +
88B VAL* 2.7 39.0 + - + +
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 2.7 51.8 + - - +
81B GLU 3.3 15.5 + - - +
82B GLN* 3.4 22.4 - - - +
83B MET 3.3 0.2 - - - -
84B LEU* 1.3 82.6 - - - +
86B LEU* 1.3 64.5 + - + +
88B VAL* 3.2 6.0 + - - +
89B LEU 3.2 18.4 + - - -
112B PRO* 3.4 30.6 - - + +
113B GLU* 4.4 9.9 - - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PRO* 5.0 4.9 - - + -
72B TRP* 3.6 54.9 - - + +
73B LEU* 4.0 17.7 - - + -
78B ARG* 3.5 33.9 - - - +
82B GLN 3.2 14.5 + - - +
83B MET* 3.7 7.2 - - - +
84B LEU 3.3 0.2 - - - -
85B GLU* 1.3 81.6 - - + +
87B LEU* 1.3 62.2 + - - +
89B LEU* 3.3 11.2 - - - +
90B GLU* 3.2 18.7 + - - +
110B GLY 4.1 19.1 - - - +
112B PRO* 5.3 1.1 - - + -
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.4 12.2 - - + -
69A CYS* 4.9 0.2 - - + -
72A TRP* 3.3 42.8 - - + -
73A LEU* 3.4 29.2 - - + -
87A LEU* 3.5 43.1 - - + -
90A GLU* 4.5 4.3 - - + +
83B MET 3.0 17.1 + - - +
84B LEU 3.6 2.5 - - - +
86B LEU* 1.3 76.9 - - - +
88B VAL* 1.3 63.7 + - - +
90B GLU* 3.2 23.5 - - + +
91B GLN 3.2 5.2 + - - -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 4.1 8.5 - - - -
62A LEU* 3.8 25.6 - - + +
65A LEU* 3.6 26.6 - - + +
66A ARG* 3.6 21.5 - - + +
69A CYS* 3.4 20.2 - - - -
84B LEU 2.7 35.9 + - - +
85B GLU* 3.5 10.5 - - - +
87B LEU* 1.3 73.3 - - - +
89B LEU* 1.3 57.9 + - - +
91B GLN* 3.3 2.8 + - - +
92B PHE* 2.9 30.1 + - - +
112B PRO* 4.4 5.4 - - + -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG* 3.9 24.5 - - - +
85B GLU 3.2 9.5 + - - +
86B LEU* 3.3 13.7 - - - +
88B VAL* 1.3 78.9 - - - +
90B GLU* 1.3 59.2 + - - +
92B PHE* 3.5 4.1 - - - +
93B LEU* 2.9 69.8 + - + +
109B PRO* 4.5 2.9 - - + -
110B GLY* 4.0 17.7 - - - +
111B SER 3.5 29.8 - - - +
112B PRO* 3.6 20.3 - - + +
115B ALA* 3.7 4.0 - - + -
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ARG* 3.6 12.6 + - - +
87A LEU* 4.8 4.9 - - + -
44B ARG* 2.8 42.2 + - - +
47B PHE* 5.0 1.7 - - - -
48B ARG* 2.8 43.8 + - - +
72B TRP* 4.2 7.7 - - + -
86B LEU 3.2 10.2 + - - +
87B LEU* 3.2 24.7 - - + +
88B VAL 3.2 0.2 - - - -
89B LEU* 1.3 86.7 - - - +
91B GLN* 1.3 62.7 + - - +
93B LEU* 3.6 3.9 + - - +
94B GLY* 3.5 12.1 + - - -
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PHE* 2.9 61.0 + - + +
48A ARG* 3.3 49.3 + - - +
50A PHE* 3.1 21.6 + - - +
65A LEU* 3.9 9.6 - - + +
87B LEU 3.2 3.4 + - - -
90B GLU* 1.3 78.0 - - - +
92B PHE* 1.3 60.6 + - - +
94B GLY 3.0 4.0 + - - -
95B ALA* 2.8 42.0 + - - +
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Residues in contact with PHE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PHE* 5.8 0.4 - + - -
52A TYR* 3.9 17.7 - + + +
58A PRO* 3.3 47.3 - - + -
61A ALA* 4.6 2.0 - - + -
62A LEU* 3.6 20.9 - - + -
65A LEU* 3.9 19.9 - - + +
88B VAL 2.9 17.9 + - - +
89B LEU* 3.5 6.1 - - + +
91B GLN* 1.3 77.4 - - - +
93B LEU* 1.3 76.6 + - + +
95B ALA* 3.2 13.7 + - + +
96B LEU* 3.2 28.0 + - + +
112B PRO 4.2 1.8 - - - -
115B ALA* 3.8 11.7 - - + -
116B ALA* 3.7 22.2 - - + -
119B VAL* 3.7 11.0 - - + -
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG* 3.9 9.2 - - - +
89B LEU* 2.9 42.3 + - + +
90B GLU* 4.0 5.2 - - - +
91B GLN 3.2 0.2 - - - -
92B PHE* 1.3 83.7 - - + +
94B GLY* 1.3 58.4 + - - +
96B LEU* 3.3 17.6 - - + +
101B GLN* 2.9 26.2 + - + +
104B VAL* 3.6 25.4 - - + -
105B GLN* 3.4 30.1 - - - +
108B ARG* 6.1 1.1 - - - -
109B PRO* 5.0 3.6 - - + -
115B ALA* 3.5 30.7 - - + -
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Residues in contact with GLY 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ARG* 5.2 4.9 - - - -
90B GLU 3.5 7.8 + - - -
91B GLN* 3.0 12.4 + - - -
93B LEU* 1.3 75.5 - - - +
95B ALA* 1.3 62.3 + - - +
96B LEU 3.3 6.3 - - - +
101B GLN* 3.3 16.4 + - - -
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PHE* 3.8 10.8 - - + +
51A HIS* 4.7 2.7 - - - +
52A TYR* 3.1 40.3 + - + +
91B GLN* 2.8 34.1 + - - +
92B PHE* 3.2 10.1 + - + +
94B GLY* 1.3 76.3 - - - +
96B LEU* 1.3 65.1 + - - +
97B PRO* 3.8 0.9 - - - +
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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