Contacts of the helix formed by residues 58 - 77 (chain B) in PDB entry 4F4I
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 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ASP 3.8 2.2 + - - -
57B MET* 1.3 73.9 - - - +
59B ILE* 1.3 55.6 + - - +
60B ARG* 2.6 41.2 + - - +
61B THR* 3.1 27.6 + - - +
62B GLU* 2.8 30.5 + - - +
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Residues in contact with ILE 59 (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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57B MET 4.3 4.9 - - - +
58B ASP* 1.3 72.3 + - - +
60B ARG* 1.3 62.9 + - + +
62B GLU* 3.3 10.3 - - - +
63B ALA* 2.7 35.9 + - - +
101B GLN* 4.5 3.1 - - + +
105B ARG* 3.4 58.1 - - + +
106B GLY 5.6 1.1 - - - -
107B ILE* 3.7 29.6 - - + +
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Residues in contact with ARG 60 (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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58B ASP* 2.6 21.1 + - - +
59B ILE* 1.3 73.3 - - + +
61B THR* 1.3 63.0 + - - +
63B ALA* 3.8 2.9 - - - +
64B MET* 2.9 37.8 + - + +
107B ILE* 3.7 42.2 + - + +
111B GLU* 2.9 38.0 + - - +
115B LEU* 5.2 0.2 - - - +
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Residues in contact with THR 61 (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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57B MET* 3.8 29.3 - - + +
58B ASP* 3.1 26.3 + - - +
60B ARG* 1.3 73.0 - - - +
62B GLU* 1.3 64.2 + - - +
64B MET* 3.2 16.0 + - + +
65B LEU* 3.0 37.1 + - + +
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Residues in contact with GLU 62 (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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51B VAL* 3.7 27.1 - - + +
57B MET* 4.2 20.9 + - - +
58B ASP 2.8 12.2 + - - +
59B ILE* 3.3 12.1 - - - +
61B THR* 1.3 77.2 - - - +
63B ALA* 1.3 61.5 + - - +
65B LEU* 3.5 2.1 + - - +
66B PHE* 3.1 52.8 + - + -
101B GLN* 4.1 8.1 + - - +
105B ARG* 2.9 33.5 + - - -
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Residues in contact with ALA 63 (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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59B ILE 2.7 19.2 + - - +
60B ARG* 3.3 3.8 + - - +
62B GLU* 1.3 72.9 - - - +
64B MET* 1.3 58.3 + - - +
66B PHE* 3.4 7.2 + - - +
67B ALA* 2.9 28.8 + - - +
97B SER* 6.3 0.4 - - - -
101B GLN* 3.7 29.6 - - + +
107B ILE* 4.3 9.0 - - + -
112B VAL* 5.5 4.7 - - + -
115B LEU* 3.6 17.4 - - + +
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Residues in contact with MET 64 (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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60B ARG* 2.9 35.2 + - + +
61B THR* 3.7 11.9 - - + +
63B ALA* 1.3 76.7 - - - +
65B LEU* 1.3 58.8 + - + +
67B ALA* 3.3 3.0 + - - +
68B ALA* 2.9 29.7 + - - +
115B LEU* 3.6 29.6 - - + -
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Residues in contact with LEU 65 (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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47B ILE* 3.1 30.1 - - + +
48B ARG* 6.0 0.4 - - - -
50B ILE* 4.0 29.6 - - + -
51B VAL* 3.6 30.3 - - + -
57B MET* 4.3 4.0 - - + -
61B THR* 3.0 37.5 + - + +
64B MET* 1.3 77.0 - - + +
66B PHE* 1.3 58.8 + - - +
68B ALA* 3.4 5.1 + - + -
69B SER* 2.8 24.7 + - - -
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Residues in contact with PHE 66 (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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37B GLU* 5.5 0.5 - - - +
48B ARG* 4.3 25.4 - - + -
51B VAL* 3.9 19.3 - - + -
52B LEU* 5.4 5.8 - - + -
62B GLU* 3.1 52.8 + - + +
63B ALA* 3.5 5.8 - - - +
65B LEU* 1.3 73.7 - - - +
67B ALA* 1.3 61.1 + - - +
69B SER* 3.3 6.7 + - - -
70B ARG* 2.8 34.6 + - - +
92B ARG* 4.3 26.9 - - - -
97B SER* 5.3 7.0 - - - +
101B GLN* 4.2 18.6 - - - +
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Residues in contact with ALA 67 (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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63B ALA 2.9 17.4 + - - +
64B MET 3.6 4.3 - - - +
66B PHE* 1.3 75.1 - - - +
68B ALA* 1.3 58.5 + - - +
70B ARG* 3.3 10.4 + - - +
71B ARG 2.9 23.7 + - - -
115B LEU* 4.0 24.0 - - + -
116B ASN* 4.1 13.9 - - - +
119B ALA* 3.6 26.9 - - + +
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Residues in contact with ALA 68 (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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47B ILE* 4.3 15.0 - - + -
64B MET 2.9 17.2 + - - +
65B LEU* 3.6 10.5 - - + +
67B ALA* 1.3 76.3 - - - +
69B SER* 1.3 55.4 + - - +
71B ARG* 3.2 8.0 + - - +
72B GLU* 3.0 32.6 + - - +
119B ALA* 5.4 0.4 - - - -
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Residues in contact with SER 69 (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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37B GLU* 5.4 1.0 - - - +
38B PRO* 3.7 12.7 - - - +
44B GLY* 2.6 38.1 + - - -
47B ILE* 3.8 11.0 - - - +
48B ARG* 3.8 10.3 - - - +
65B LEU 2.8 18.1 + - - -
66B PHE* 3.6 11.0 - - - -
68B ALA* 1.3 75.9 - - - +
70B ARG* 1.3 64.5 + - - +
72B GLU* 3.4 3.5 + - - +
73B HIS* 3.2 22.2 + - - +
92B ARG* 5.9 0.5 + - - -
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Residues in contact with ARG 70 (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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37B GLU* 2.8 48.9 + - - +
66B PHE* 2.8 23.5 + - - +
67B ALA* 3.3 10.8 - - - +
69B SER* 1.3 72.9 - - - +
71B ARG* 1.3 56.9 + - - +
73B HIS* 3.5 4.9 + - - +
74B LEU* 2.9 26.3 + - - +
92B ARG* 3.9 8.3 - - - +
93B TYR* 2.8 58.8 + - + +
94B ILE* 3.8 5.0 - - - +
96B SER* 4.5 2.4 - - - -
97B SER* 2.7 30.3 + - - -
116B ASN* 3.1 22.6 + - - -
119B ALA* 5.4 1.1 - - + -
120B ILE* 4.2 15.9 - - + -
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Residues in contact with ARG 71 (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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67B ALA 2.9 14.1 + - - +
68B ALA* 3.6 10.1 - - - +
70B ARG* 1.3 73.7 - - - +
72B GLU* 1.3 70.9 + - - +
74B LEU* 3.1 7.5 + - - +
75B VAL* 2.9 50.2 + - + +
118B PHE* 4.7 7.4 + - - -
119B ALA* 2.9 42.7 + - + +
120B ILE* 4.4 2.2 - - - +
121B ASN* 3.9 31.7 - - - +
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Residues in contact with GLU 72 (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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41B VAL* 4.3 4.3 - - + -
43B THR* 2.8 43.8 + - + +
44B GLY* 3.7 14.8 - - - +
47B ILE* 3.9 8.5 - - + -
68B ALA 3.0 16.4 + - - +
69B SER 3.6 8.5 - - - +
71B ARG* 1.3 77.3 - - - +
73B HIS* 1.3 56.8 + - - +
75B VAL* 3.4 4.5 + - - +
76B LEU* 2.9 51.2 + - - +
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Residues in contact with HIS 73 (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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35B THR* 3.0 46.1 - - + +
37B GLU* 3.9 23.8 - - + -
38B PRO* 2.7 41.4 + - + +
39B GLY* 3.8 1.3 - - - -
41B VAL* 4.2 10.7 - - - +
44B GLY* 5.1 0.2 - - - -
69B SER 3.2 10.4 + - - +
70B ARG 3.6 7.2 - - - +
72B GLU* 1.3 75.5 - - - +
74B LEU* 1.3 68.3 + - + +
77B LYS* 3.0 30.3 + - + +
78B VAL* 3.1 23.0 + - + +
90B CYS* 3.8 12.6 - - - -
93B TYR* 6.1 2.9 - + - -
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Residues in contact with LEU 74 (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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4B PHE* 4.4 2.9 - - + -
70B ARG 2.9 15.3 + - - +
71B ARG* 3.1 13.7 + - - +
73B HIS* 1.3 78.0 - - - +
75B VAL* 1.3 60.3 + - + +
78B VAL* 3.1 32.1 + - + -
79B ILE* 2.9 42.4 + - + +
93B TYR* 3.5 30.1 - - + +
119B ALA 4.4 3.6 - - - +
120B ILE* 3.8 35.0 - - + +
123B LEU* 3.4 27.8 - - + -
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Residues in contact with VAL 75 (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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71B ARG* 2.9 56.0 + - + +
72B GLU* 4.4 5.4 - - - +
74B LEU* 1.3 80.4 - - + +
76B LEU* 1.3 66.5 + - + +
79B ILE* 4.1 21.7 - - + +
80B PRO* 3.5 16.3 - - - +
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Residues in contact with LEU 76 (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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41B VAL* 3.7 30.3 - - + +
42B PRO* 6.1 0.2 - - + -
43B THR* 5.0 4.7 - - - +
72B GLU* 2.9 38.8 + - - +
75B VAL* 1.3 88.0 - - + +
77B LYS* 1.3 59.7 + - - +
80B PRO* 3.6 12.4 - - - +
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Residues in contact with LYS 77 (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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33B ILE* 5.1 12.6 - - + +
34B MET 5.2 1.9 + - - -
35B THR* 2.9 35.9 + - + +
39B GLY* 2.6 33.0 + - - +
41B VAL* 3.8 13.9 - - + -
73B HIS* 3.0 20.2 + - + +
75B VAL 3.5 0.8 - - - -
76B LEU* 1.3 81.2 - - - +
78B VAL* 1.3 68.2 + - + +
80B PRO* 3.5 6.3 - - - +
81B ALA* 3.4 21.5 + - - +
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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