Contacts of the helix formed by residues 58 - 75 (chain F) in PDB entry 5FLM
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 58 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875A TYR* 5.6 1.5 + - + -
1082A HIS* 3.8 23.3 - - + +
1083A PRO* 3.6 43.7 + - + +
54F THR* 5.2 2.2 - - - +
56F TYR 3.6 6.2 + - - +
57F MET* 1.3 81.2 - - - +
59F LYS* 1.3 66.2 + - - +
60F TYR* 3.2 7.6 + - - +
61F GLU* 3.1 35.0 + - - +
62F ARG* 3.1 19.8 + - - +
108F ARG* 5.2 3.1 - - - +
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Residues in contact with LYS 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A GLU 4.9 0.6 - - - +
518A LEU* 4.1 15.4 - - + +
899A GLU* 3.7 22.8 + - - -
1082A HIS* 3.5 34.9 + - + +
1085A GLU* 4.9 6.2 + - - +
57F MET 3.9 0.6 + - - -
58F THR* 1.3 72.4 - - - +
60F TYR* 1.3 90.2 + - + +
62F ARG* 3.4 25.9 + - - +
63F ALA* 2.9 28.4 + - - +
126F THR* 5.6 1.9 - - - +
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Residues in contact with TYR 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A LEU* 3.7 20.2 - - + -
1082A HIS* 5.0 1.6 - - + -
1083A PRO 4.2 10.5 - - - -
1084A GLY* 3.4 10.5 - - - -
1085A GLU* 3.4 48.8 - - + +
1086A MET 4.4 2.3 + - - -
1467A GLY* 3.6 12.3 - - - -
1468A THR* 3.5 23.6 + - - +
1471A PHE* 4.0 5.4 - - + -
1096B ALA 4.4 3.8 + - - -
1097B HIS 3.4 27.8 + - - -
1098B GLY* 3.8 19.8 - - - -
58F THR* 3.1 6.2 - - - +
59F LYS* 1.3 91.0 - - + +
61F GLU* 1.3 60.2 + - - +
63F ALA* 3.2 4.8 + - - +
64F ARG* 2.9 28.6 + - - +
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Residues in contact with GLU 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875A TYR* 3.8 11.1 + - - +
1471A PHE* 3.5 27.6 - - + -
57F MET* 3.8 7.9 - - + +
58F THR* 3.1 27.4 + - - +
60F TYR* 1.3 76.8 - - - +
62F ARG* 1.3 57.6 + - - +
64F ARG* 4.3 0.2 - - - +
65F VAL* 2.9 37.7 + - - +
106F ILE* 3.7 26.7 - - + +
108F ARG* 2.5 59.0 + - - +
123F LEU* 3.8 0.2 - - - +
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Residues in contact with ARG 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A GLU* 3.2 50.1 + - - +
523A ARG* 3.3 36.6 - - - +
57F MET* 3.6 19.6 - - + +
58F THR 3.1 12.1 + - - +
59F LYS* 3.6 22.2 + - - +
61F GLU* 1.3 75.8 - - - +
63F ALA* 1.3 61.0 + - - +
65F VAL* 3.8 1.7 - - - +
66F LEU* 3.0 40.2 + - + +
94F MET* 5.2 8.2 - - - +
97F LEU* 3.9 16.8 - - + -
125F ILE* 5.3 5.8 - - - -
126F THR* 4.5 17.6 + - - +
127F ASP* 5.0 11.3 + - - -
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Residues in contact with ALA 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A ALA* 4.4 4.8 - - - +
514A GLU* 4.3 17.8 + - + +
517A GLU* 3.2 19.7 + - + +
518A LEU* 3.9 30.1 - - + -
1468A THR* 4.5 1.3 - - - +
59F LYS 2.9 15.3 + - - +
60F TYR 3.4 8.1 - - - +
62F ARG* 1.3 76.8 - - - +
64F ARG* 1.3 64.0 + - - +
66F LEU* 3.2 1.0 + - - +
67F GLY* 2.9 19.8 + - - -
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Residues in contact with ARG 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510A GLU* 4.6 1.8 + - - +
514A GLU* 4.9 5.8 - - - -
1463A LEU* 3.7 26.6 - - - +
1468A THR* 2.6 54.2 + - + -
1469A GLY* 4.2 1.4 - - - -
1471A PHE* 3.4 48.1 + - + -
1472A ASP* 4.8 9.3 + - - -
1473A LEU* 3.7 23.7 - - + +
1101B GLN* 3.6 25.1 - - - +
60F TYR 2.9 9.3 + - - +
63F ALA* 1.3 74.1 - - - +
65F VAL* 1.3 56.8 + - - +
67F GLY* 3.2 1.8 + - - +
68F THR* 2.9 36.5 + - - +
59G ILE 4.9 4.6 + - - -
60G GLN 5.4 0.2 - - - -
61G PRO* 4.2 17.0 - - - +
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Residues in contact with VAL 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1473A LEU* 3.7 31.2 - - + -
57F MET* 5.0 3.1 - - + -
61F GLU* 2.9 25.6 + - - +
62F ARG* 3.8 4.9 - - - +
64F ARG* 1.3 77.2 - - - +
66F LEU* 1.3 61.4 + - + +
68F THR* 3.3 2.5 + - - -
69F ARG* 2.9 27.7 + - - +
97F LEU* 5.0 3.6 - - + -
102F ILE* 4.3 32.1 - - + -
104F ILE* 4.4 7.1 - - + +
106F ILE* 3.7 19.1 - - + -
120F VAL* 4.4 15.7 - - + -
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Residues in contact with LEU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A ALA* 4.1 5.2 - - + +
517A GLU* 3.0 38.8 - - - +
62F ARG* 3.0 18.1 + - + +
63F ALA 3.9 0.4 - - - +
65F VAL* 1.3 75.1 - - + +
67F GLY* 1.3 59.5 + - - +
69F ARG* 4.5 1.1 - - - +
70F ALA* 2.9 31.0 + - - +
90F LEU* 4.8 1.0 - - + +
93F ALA* 3.3 39.3 - - + +
94F MET* 3.5 15.5 - - + -
97F LEU* 3.5 27.6 - - + -
102F ILE* 3.7 20.2 - - + -
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Residues in contact with GLY 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510A GLU* 3.7 28.3 - - - -
513A ALA* 3.6 19.6 - - - +
63F ALA 2.9 13.3 + - - -
64F ARG* 3.2 3.6 + - - -
66F LEU* 1.3 77.6 - - - +
68F THR* 1.3 55.4 + - - +
70F ALA* 3.4 2.6 + - - +
71F LEU* 2.9 29.1 + - - +
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Residues in contact with THR 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A GLU* 3.7 16.0 + - - +
1473A LEU* 3.3 20.1 - - + +
64F ARG* 2.9 19.8 + - - +
65F VAL 3.7 3.4 - - - -
67F GLY* 1.3 75.1 - - - +
69F ARG* 1.3 59.1 + - - +
71F LEU* 3.1 9.5 + - + +
72F GLN* 2.9 43.5 + - + +
104F ILE* 4.2 12.6 - - + -
59G ILE* 3.8 28.3 - - + +
64G GLY* 6.2 0.9 - - - -
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Residues in contact with ARG 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F VAL 2.9 18.0 + - - +
66F LEU* 4.6 0.2 - - - -
68F THR* 1.3 76.4 - - - +
70F ALA* 1.3 58.8 + - - +
72F GLN* 3.3 27.4 + - - +
73F ILE* 2.9 53.0 + - + +
77F ALA* 4.8 4.9 - - - +
78F PRO 3.2 26.5 + - - -
79F VAL* 3.6 7.1 - - - +
80F MET* 3.7 11.9 - - - +
93F ALA* 4.1 12.8 - - + -
96F GLU* 2.4 48.7 + - - +
102F ILE* 4.1 20.9 - - + -
103F PRO* 4.3 26.5 - - - +
104F ILE* 4.7 4.0 - - + +
18G PHE* 6.0 2.6 - - - +
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Residues in contact with ALA 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A LEU* 4.8 7.0 - - + +
66F LEU 2.9 22.7 + - - +
67F GLY* 3.6 5.2 - - - +
69F ARG* 1.3 76.8 - - - +
71F LEU* 1.3 56.1 + - - +
73F ILE* 3.5 0.6 + - - -
74F ALA* 2.9 30.5 + - - +
89F PRO* 3.4 26.1 - - + +
90F LEU* 3.6 28.9 - - + -
93F ALA* 4.0 4.0 - - + +
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Residues in contact with LEU 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ILE* 4.2 15.7 - - + -
508A SER* 5.1 9.4 - - - +
509A LEU* 5.0 10.5 - - + +
510A GLU* 4.2 18.2 - - + +
67F GLY 2.9 14.6 + - - +
68F THR* 3.5 11.2 - - + +
70F ALA* 1.3 76.8 - - - +
72F GLN* 1.3 64.0 + - + +
74F ALA* 3.0 8.4 + - + +
75F MET* 2.9 44.1 + - + +
62G GLY* 3.9 4.0 - - - -
63G ARG* 3.5 15.0 - - - +
64G GLY* 3.5 30.3 - - - +
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Residues in contact with GLN 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1475A LEU* 4.3 6.1 - - - +
68F THR* 2.9 36.2 + - + +
69F ARG* 3.8 27.6 + - - +
71F LEU* 1.3 75.4 - - + +
73F ILE* 1.3 62.8 + - - +
75F MET* 2.9 18.8 + - - +
77F ALA* 3.1 31.5 + - + +
103F PRO* 5.6 3.1 - - - +
104F ILE* 4.8 8.9 - - - +
15G PRO* 4.5 7.4 - - + -
18G PHE* 3.5 31.3 - - + -
59G ILE* 4.1 20.6 - - - +
64G GLY* 4.5 9.8 + - - +
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Residues in contact with ILE 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A THR* 4.6 3.6 - - - +
397A PHE* 5.9 5.8 - - + -
69F ARG* 2.9 60.0 + - + +
70F ALA 3.9 2.9 - - - +
72F GLN* 1.3 74.4 - - - +
74F ALA* 1.3 61.5 + - - +
75F MET 3.2 1.0 + - - -
76F CYS* 3.3 13.5 + - - -
77F ALA* 4.2 9.1 + - - +
79F VAL* 3.7 20.9 - - + -
89F PRO* 4.2 13.9 - - + +
92F ILE* 3.6 27.4 - - + -
93F ALA* 4.2 8.5 - - - +
96F GLU* 3.4 20.6 - - - +
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ILE* 3.2 25.5 - - + +
395A THR* 3.2 25.7 - - + +
509A LEU* 3.6 26.7 - - + -
70F ALA 2.9 18.8 + - - +
71F LEU* 3.4 6.3 - - - +
73F ILE* 1.3 75.7 - - - +
75F MET* 1.3 57.1 + - - +
76F CYS 3.3 1.8 - - - -
89F PRO* 3.9 11.2 - - + +
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Residues in contact with MET 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ILE* 4.1 17.3 - - + -
395A THR* 5.2 0.4 - - - -
71F LEU* 2.9 42.3 + - + +
72F GLN 2.9 8.8 + - - +
74F ALA* 1.3 78.0 - - - +
76F CYS* 1.3 64.9 + - - +
77F ALA 3.3 4.2 + - - -
14G HIS* 3.0 48.7 + - + +
15G PRO* 3.8 22.7 - - + -
16G ARG 4.6 0.7 + - - -
63G ARG* 3.3 28.5 - - - +
64G GLY* 3.9 2.9 - - - -
65G PHE* 4.7 6.3 - - + -
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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