Contacts of the helix formed by residues 61 - 77 (chain A) in PDB entry 5FV7
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 THR 61 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A THR* 1.3 71.9 - - - +
62A SER* 1.3 53.4 + - - +
63A HIS* 3.1 11.2 - - - +
64A LEU* 2.7 33.7 + - + +
65A MET* 3.3 9.8 + - - -
314A LYS* 3.8 46.5 + - + +
316A PHE* 3.1 29.2 - - - -
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Residues in contact with SER 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE* 2.7 28.2 + - - +
43A LEU* 3.8 11.5 - - - +
44A ILE 5.3 0.7 + - - -
60A THR* 3.1 18.6 - - - -
61A THR* 1.3 75.3 - - - +
63A HIS* 1.3 57.2 + - - +
65A MET* 4.0 18.6 - - - +
66A GLY* 2.9 27.2 + - - -
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Residues in contact with HIS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 4.1 15.5 - - + -
42A PHE* 3.7 16.0 - - - -
43A LEU* 3.9 12.7 - - + +
60A THR 3.7 15.1 + - - -
61A THR* 3.8 14.0 - - - +
62A SER* 1.3 79.1 + - - +
64A LEU* 1.3 72.1 + - + +
67A MET* 3.1 26.5 + - - +
136A GLN* 5.7 0.2 - - - +
137A HIS* 3.3 55.2 + + - +
140A GLU* 2.6 37.2 + - + -
141A CYS* 3.7 7.7 - - - -
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 2.7 22.4 + - - +
63A HIS* 1.3 84.8 - - + +
65A MET* 1.3 58.6 + - - +
66A GLY 3.3 0.2 - - - -
67A MET* 4.7 0.9 - - - -
68A PHE* 2.8 28.4 + - - +
140A GLU* 3.4 50.7 - - + +
141A CYS* 3.8 7.4 - - - +
144A LEU* 3.4 26.7 - - + +
309A PHE* 4.5 5.4 - - + -
310A MET* 3.7 17.2 - - + +
314A LYS* 3.6 35.2 - - + -
316A PHE* 4.5 0.4 - - + -
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Residues in contact with MET 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 3.3 2.6 + - - -
62A SER* 4.0 22.0 - - - +
64A LEU* 1.3 75.1 - - - +
66A GLY* 1.3 68.0 + - - +
68A PHE* 3.7 7.9 - - - -
69A TYR* 3.1 45.7 + - + +
316A PHE* 3.3 32.0 - - + -
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 3.8 24.5 - - - -
62A SER 2.9 19.6 + - - -
65A MET* 1.3 77.7 - - - +
67A MET* 1.3 56.4 + - - +
70A ARG* 3.0 44.8 + - - +
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Residues in contact with MET 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA 4.6 0.9 - - - +
38A SER* 3.6 24.5 - - - +
39A ILE* 3.9 9.9 - - + -
42A PHE* 3.5 15.7 - - + -
63A HIS 3.1 15.4 + - - +
64A LEU 4.0 2.7 - - - +
66A GLY* 1.3 73.6 - - - +
68A PHE* 1.3 64.6 + - - +
70A ARG* 4.8 0.4 - - - -
71A THR* 2.7 39.6 + - - +
83A TYR* 3.6 16.4 - - + +
85A PHE* 4.8 2.5 - - + -
141A CYS* 3.8 31.2 - - + +
144A LEU* 4.4 7.6 - - + -
145A LEU* 3.7 39.5 - - + -
148A MET* 4.3 1.2 - - - +
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Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU 2.8 24.3 + - - +
65A MET* 4.0 3.6 - - - -
66A GLY 3.4 0.2 - - - -
67A MET* 1.3 77.9 - - - +
69A TYR* 1.3 89.1 + + - +
72A ILE* 2.8 44.1 + - + +
144A LEU* 3.9 13.4 - - + +
148A MET* 3.7 19.5 - - + +
306A LEU* 4.0 19.3 - - + -
310A MET* 3.8 17.7 - - + -
321A ILE* 3.6 44.0 - - + -
324A GLY* 3.8 20.2 - - - -
325A VAL* 3.9 7.0 - - + -
328A LEU* 5.5 0.7 - - + -
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Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A MET* 3.1 47.2 + - + +
66A GLY 4.6 0.2 - - - +
68A PHE* 1.3 105.0 - + - +
70A ARG* 1.3 66.9 + - - +
72A ILE* 3.3 7.4 + - + +
73A ARG* 3.0 22.2 + - - +
316A PHE* 5.0 5.9 - + - -
320A ARG* 3.7 38.9 + - - +
321A ILE* 4.3 4.7 - - + +
324A GLY* 5.1 2.5 - - - -
327A ARG* 4.2 21.2 + - - -
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLN* 5.6 0.6 - - - +
42A PHE* 3.7 29.0 - - + +
66A GLY* 3.0 28.2 + - - +
67A MET 4.7 0.4 - - - +
69A TYR* 1.3 77.6 - - - +
71A THR* 1.3 58.0 + - - +
73A ARG* 3.2 14.6 + - - +
74A MET* 2.9 44.8 + - + +
83A TYR* 5.3 0.2 - - - +
194A LEU 4.6 4.7 - - - +
195A THR* 3.5 53.2 + - - +
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A MET* 2.7 25.9 + - - +
68A PHE 3.9 2.2 - - - -
70A ARG* 1.3 74.7 - - - +
72A ILE* 1.3 61.6 + - - +
74A MET* 3.3 9.1 + - - +
75A MET* 2.9 29.5 + - + +
81A PRO* 3.7 24.9 - - + -
83A TYR* 2.9 26.4 + - + -
145A LEU* 4.4 1.1 - - + +
148A MET* 4.2 9.2 - - + -
150A ILE* 3.9 27.1 - - + -
328A LEU* 5.4 0.7 - - + -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE* 2.8 44.0 - - + +
69A TYR* 3.5 10.3 - - - +
71A THR* 1.3 75.8 - - - +
73A ARG* 1.3 53.6 + - - +
75A MET* 3.1 6.1 + - - +
76A GLU* 2.8 42.5 + - + +
148A MET* 3.9 17.0 - - + -
324A GLY 3.6 27.6 - - - +
327A ARG* 3.7 33.0 - - + +
328A LEU* 3.7 30.5 - - + +
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Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 5.3 7.4 - - + -
69A TYR 3.0 13.2 + - - +
70A ARG* 3.2 19.7 + - - +
72A ILE* 1.3 76.0 - - - +
74A MET* 1.3 57.8 + - - +
76A GLU* 3.6 26.8 + - - +
77A ASN* 3.0 67.5 + - - +
327A ARG* 5.3 2.9 - - - +
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Residues in contact with MET 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 5.1 6.1 - - + -
33A ILE* 3.5 35.9 - - + -
42A PHE* 5.6 0.2 - - + -
70A ARG* 2.9 29.3 + - + +
71A THR* 3.5 9.2 - - - +
73A ARG* 1.3 75.5 - - + +
75A MET* 1.3 62.0 + - - +
77A ASN* 3.3 5.6 + - - -
78A GLY 3.2 4.7 + - - -
79A ILE* 2.9 47.4 + - + +
81A PRO* 4.2 13.0 - - + -
83A TYR* 4.0 15.0 - - - +
194A LEU* 4.1 29.4 - - + +
195A THR 4.0 20.9 - - - +
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Residues in contact with MET 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A THR* 2.9 23.6 + - + +
72A ILE* 3.5 6.3 - - - +
74A MET* 1.3 74.9 - - - +
76A GLU* 1.3 63.2 + - - +
78A GLY* 3.4 11.3 + - - -
79A ILE 3.4 6.5 - - - +
80A LYS* 4.3 8.5 - - - -
81A PRO* 3.7 28.0 - - + -
150A ILE* 4.5 2.9 - - + -
298A TRP* 4.5 16.4 - - + -
328A LEU* 4.3 22.4 - - + +
331A SER* 3.3 25.0 - - - +
332A ARG* 3.8 38.4 - - + +
335A SER* 4.0 15.6 + - - -
336A THR* 5.4 2.7 - - - +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 5.0 5.4 - - - -
72A ILE* 2.8 24.2 + - + +
73A ARG* 3.9 31.8 + - - +
75A MET* 1.3 71.6 - - - +
77A ASN* 1.3 60.5 + - - +
78A GLY* 3.1 8.3 + - - -
327A ARG* 2.7 55.8 + - - +
331A SER* 3.9 17.8 - - - +
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Residues in contact with ASN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.7 52.3 - - + +
24A LYS* 4.6 11.8 - - - +
27A PHE* 3.8 19.6 - - - +
73A ARG* 3.0 53.2 + - - +
74A MET 3.3 4.4 + - - +
76A GLU* 1.3 75.4 + - - +
78A GLY* 1.3 54.6 + - - +
79A ILE* 3.3 8.5 + - + +
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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