Contacts of the helix formed by residues 87 - 101 (chain A) in PDB entry 5M64
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 ASN 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A TYR* 1.3 80.6 - - - +
88A PRO* 1.3 59.8 - - - +
89A LEU* 3.0 28.9 + - - +
90A PHE* 2.7 30.3 + - + +
91A PHE* 2.4 38.8 + - - +
94A LEU* 6.2 0.8 - - - +
355A PHE 3.9 15.7 + - - +
357A MET* 4.0 24.7 - - + +
438A ILE* 4.5 6.0 - - - +
1192B MET 3.9 18.0 + - - -
1193B GLY* 4.9 0.6 - - - -
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Residues in contact with PRO 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A CYS* 6.3 0.2 - - - -
86A TYR* 4.5 3.4 - - + +
87A ASN* 1.3 89.6 - - - +
89A LEU* 1.3 60.5 + - + +
90A PHE 3.1 1.0 + - - -
91A PHE* 3.9 13.3 + - + -
92A ASN* 4.3 12.1 + - - +
248A PHE* 6.6 0.2 - - + -
431A GLN* 5.8 0.9 - - - +
435A ASN* 4.6 13.2 - - + -
438A ILE* 3.6 31.0 - - + -
439A ASP* 4.8 13.9 - - + +
442A LYS* 5.0 6.5 - - + -
1623A THR* 5.2 1.4 - - - +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASN* 3.0 16.3 + - - +
88A PRO* 1.3 77.7 - - + +
90A PHE* 1.3 73.1 + - + +
92A ASN* 5.4 0.4 - - - -
93A GLN* 4.6 2.0 - - - +
438A ILE* 4.3 16.4 - - + +
457A LYS* 6.2 2.9 - - + -
1619A CYS* 4.7 18.4 - - + +
1623A THR* 3.1 43.2 - - + +
1192B MET* 3.3 59.2 - - + +
1194B ILE* 4.6 4.5 - - + -
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Residues in contact with PHE 90 (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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18A ILE* 4.2 22.4 - - + -
87A ASN* 2.7 37.1 + - + +
89A LEU* 1.3 81.9 - - + +
91A PHE* 1.3 57.7 + - - +
92A ASN 3.2 2.9 - - - -
93A GLN* 2.9 24.7 + - + +
94A LEU* 3.0 16.6 + - + +
354A SER 4.6 2.5 - - - -
355A PHE* 3.5 46.9 - + + +
357A MET* 5.8 0.7 - - + -
1623A THR* 4.7 4.9 - - - -
1626A VAL* 4.2 12.3 - - + -
1627A LEU* 4.3 33.2 - - + -
1193B GLY 5.6 0.2 - - - -
1194B ILE* 3.6 30.7 - - + -
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Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR* 4.3 28.3 - + + -
87A ASN 2.4 35.9 + - - +
88A PRO* 3.9 8.2 + - + -
90A PHE* 1.3 68.7 - - - +
92A ASN* 1.3 61.1 + - + +
93A GLN 3.1 3.3 + - - -
94A LEU* 3.6 14.8 - - + +
95A TYR* 3.1 66.9 + + - +
98A LEU* 6.3 0.2 - - + -
245A LYS* 6.1 4.7 - - + -
247A GLY* 6.3 1.1 - - - -
248A PHE* 5.4 11.2 - - - -
249A THR* 5.7 7.4 - - - -
251A ILE* 4.3 24.7 - - + -
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Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PRO 4.3 9.8 + - - +
89A LEU 6.2 0.2 - - - -
90A PHE 3.2 0.8 - - - -
91A PHE* 1.3 83.6 - - + +
93A GLN* 1.3 72.5 + - + +
95A TYR* 4.9 1.8 - - - -
96A ILE* 3.5 21.8 - - - +
224A HIS* 5.6 0.2 - - - -
58S A 5.5 2.0 + - - -
59S G 4.9 7.9 + - - -
16T C 5.4 7.4 - - - +
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Residues in contact with GLN 93 (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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89A LEU 4.6 5.6 - - - +
90A PHE* 2.9 21.8 + - + +
92A ASN* 1.3 96.8 + - + +
94A LEU* 1.3 62.6 + - - +
95A TYR 3.2 1.9 + - - -
96A ILE* 3.5 16.0 + - - +
97A TYR* 3.7 14.7 - - - -
224A HIS* 4.3 17.5 + - - -
355A PHE* 5.9 0.2 - - + -
1620A GLN* 6.1 0.3 - - - +
1623A THR* 4.5 18.2 + - - +
1624A LYS* 4.3 18.4 + - - +
1627A LEU* 3.3 48.0 - - + +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR* 6.5 1.3 - - + -
87A ASN 6.2 0.9 - - - +
90A PHE* 3.0 30.6 + - + +
91A PHE* 3.6 22.9 - - + +
93A GLN* 1.3 72.3 - - - +
95A TYR* 1.3 62.2 + - - +
96A ILE 3.1 2.5 - - - -
97A TYR* 3.0 20.1 + - + +
98A LEU* 2.8 27.0 + - + +
324A LEU* 4.5 18.1 - - + +
328A PHE* 5.7 0.4 - - + -
355A PHE* 3.6 52.2 - - + +
356A PHE* 4.3 23.6 - - + -
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Residues in contact with TYR 95 (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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91A PHE* 3.1 51.2 + + + +
92A ASN* 4.9 3.6 - - - -
93A GLN 3.2 0.4 - - - -
94A LEU* 1.3 76.1 - - - +
96A ILE* 1.3 61.8 + - + +
98A LEU* 3.4 28.5 - - + -
99A ARG* 2.8 69.9 + - + +
243A PHE* 3.0 31.7 + - + +
245A LYS* 3.2 25.3 - - + +
251A ILE* 3.2 24.6 - - + +
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Residues in contact with ILE 96 (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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92A ASN* 3.5 27.4 - - - +
93A GLN 3.7 10.5 - - - +
94A LEU 3.1 0.4 - - - -
95A TYR* 1.3 79.3 - - + +
97A TYR* 1.3 69.9 + - + +
99A ARG* 3.4 29.6 - - - +
100A ALA* 3.0 31.6 + - + +
223A PHE* 4.7 7.2 - - + +
224A HIS* 3.5 40.6 - - + +
228A LEU* 3.7 20.4 - - + -
59S G 4.6 9.4 - - - +
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Residues in contact with TYR 97 (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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93A GLN 3.7 21.1 - - - -
94A LEU* 3.0 16.7 + - + +
96A ILE* 1.3 86.2 - - + +
98A LEU* 1.3 58.8 + - - +
100A ALA* 4.4 4.3 - - - +
101A SER* 2.9 35.8 + - - +
108A PHE* 3.4 36.1 - + + -
220A VAL* 5.4 4.9 - - - +
224A HIS* 5.6 6.0 - + - -
324A LEU* 4.9 15.6 - - + +
327A VAL* 6.3 0.7 - - + -
328A PHE* 5.4 7.9 - + + -
335A LEU* 5.2 7.4 - - + -
338A VAL* 3.6 26.6 - - + +
339A PHE* 3.6 38.3 - + - -
355A PHE* 5.7 0.7 - + - -
1627A LEU* 5.8 1.1 - - + -
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Residues in contact with LEU 98 (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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91A PHE* 6.3 0.7 - - + -
94A LEU* 2.8 20.2 + - + +
95A TYR* 3.1 36.1 + - + +
97A TYR* 1.3 74.9 - - - +
99A ARG* 1.3 56.8 + - - +
100A ALA 3.8 0.2 + - - -
101A SER* 4.4 7.0 + - - +
243A PHE* 3.1 52.3 - - + -
251A ILE* 4.6 9.9 - - + -
320A VAL* 4.1 21.3 - - + -
323A ILE* 5.1 9.9 - - + -
324A LEU* 4.1 27.5 - - + +
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Residues in contact with ARG 99 (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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95A TYR* 2.8 61.5 + - + +
96A ILE* 3.4 26.9 - - - +
98A LEU* 1.3 73.6 - - - +
100A ALA* 1.3 58.3 + - - +
101A SER 4.8 0.2 - - - -
109A ARG* 2.9 24.3 + - - +
224A HIS 5.7 0.6 + - - -
228A LEU* 3.5 37.7 - - + +
242A LYS* 6.2 1.8 - - - +
243A PHE* 3.7 23.3 - - + +
245A LYS* 3.7 21.7 - - - +
59S G 3.9 29.8 + - - -
60S C 5.6 2.7 + - - -
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Residues in contact with ALA 100 (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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96A ILE* 3.0 20.2 + - + +
97A TYR* 4.4 3.6 - - + +
99A ARG* 1.3 76.6 - - - +
101A SER* 1.3 64.5 + - - +
102A CYS 3.5 0.2 + - - -
108A PHE* 4.5 10.0 - - + -
109A ARG* 3.1 41.2 + - - +
110A LEU* 6.3 2.7 - - + -
227A LEU* 5.8 2.0 - - + -
228A LEU* 3.8 27.1 - - + -
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Residues in contact with SER 101 (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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97A TYR* 2.9 19.3 + - - -
98A LEU* 4.4 8.8 + - - +
99A ARG 3.7 0.9 - - - -
100A ALA* 1.3 79.8 - - - +
102A CYS* 1.3 71.1 + - - +
103A LEU* 3.8 1.0 + - - +
107A HIS 3.9 8.3 + - - -
108A PHE* 4.2 14.9 - - - -
109A ARG* 3.9 5.6 + - - -
243A PHE* 5.0 6.8 - - - -
323A ILE* 4.8 8.2 - - - +
324A LEU* 6.1 1.1 - - - -
327A VAL* 3.3 36.3 - - - +
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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
------------------------------------------------------------
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