Contacts of the helix formed by residues 84 - 96 (chain A) in PDB entry 5DSG
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 PHE 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 3.1 26.8 + - + +
83A ALA* 1.3 92.4 - - + +
85A SER* 1.3 67.8 + - - +
86A MET 3.4 0.8 + - - -
87A ASN* 3.4 2.6 + - - +
88A LEU* 3.1 36.6 + - + +
111A LEU* 3.9 18.4 - - + -
1202A OLA 5.8 3.6 - - + -
1203A OLA 4.0 23.6 - - + -
1209A OLA 3.8 55.0 - - + -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 3.8 2.9 + - - +
81A ILE* 3.2 26.4 + - - +
84A PHE* 1.3 77.6 - - - +
86A MET* 1.3 63.8 + - - +
88A LEU 3.4 0.2 + - - -
89A TYR* 2.9 26.2 + - - +
108A TRP* 3.7 10.0 + - - +
111A LEU* 4.7 6.6 - - - +
112A ASP* 2.5 34.3 + - - -
443A TYR* 3.6 21.9 + - - -
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Residues in contact with MET 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR 5.2 0.2 - - - +
42A LEU* 4.1 3.4 - - + +
43A SER* 3.7 34.3 - - - -
46A THR* 3.5 10.5 - - + +
81A ILE* 3.2 13.0 + - + +
82A GLY* 4.0 17.3 - - - +
84A PHE 3.4 0.4 - - - -
85A SER* 1.3 78.8 - - - +
87A ASN* 1.3 58.7 + - - +
89A TYR 3.3 0.2 + - - -
90A THR* 2.9 34.5 + - - +
440A TRP* 3.5 36.6 - - + -
443A TYR* 3.6 39.5 - - + +
444A VAL* 4.6 1.8 - - + +
447A THR* 3.4 24.2 - - - +
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Residues in contact with ASN 87 (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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39A THR 5.3 0.3 - - - +
40A GLY* 5.2 4.7 - - - -
43A SER* 3.4 28.6 + - - -
83A ALA* 2.6 26.2 + - - +
84A PHE 3.4 5.5 + - - +
85A SER 3.4 0.6 - - - -
86A MET* 1.3 75.1 - - - +
88A LEU* 1.3 58.7 + - - +
90A THR* 2.4 24.3 + - - +
91A VAL* 2.9 21.1 + - - +
1203A OLA 4.0 22.4 - - + +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 3.1 32.9 + - + +
85A SER 3.9 2.5 - - - +
87A ASN* 1.3 75.3 - - - +
89A TYR* 1.3 63.9 + - - +
91A VAL* 3.1 9.9 + - - +
92A TYR* 3.0 21.0 + - - +
98A TRP* 4.0 10.4 - - + -
100A LEU* 3.8 23.6 - - + -
104A VAL* 4.9 3.1 - - + -
108A TRP* 3.4 42.8 - - + +
111A LEU* 5.5 3.1 - - + -
1202A OLA 4.1 12.3 - - + -
1203A OLA 3.7 35.2 - - + -
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Residues in contact with TYR 89 (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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85A SER 2.9 19.0 + - - +
86A MET 3.6 3.4 - - - +
88A LEU* 1.3 77.7 - - - +
90A THR* 1.3 57.2 + - - +
92A TYR* 3.2 14.0 + + + +
93A ILE* 2.9 55.5 + - + +
108A TRP* 3.5 28.2 - + + -
436A SER* 3.1 34.8 + - - -
439A TYR* 3.7 13.7 - + - +
440A TRP* 3.6 38.6 - + + -
443A TYR* 3.9 12.8 - + + -
1205A P6G 3.3 31.1 - - - -
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Residues in contact with THR 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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35A ILE* 5.3 1.3 - - + -
39A THR* 3.4 41.7 - - + +
86A MET 2.9 16.9 + - - +
87A ASN* 2.4 33.5 + - - +
89A TYR* 1.3 73.2 - - - +
91A VAL* 1.3 60.5 + - - +
93A ILE* 4.2 9.0 - - + -
94A ILE* 2.9 45.5 + - - +
440A TRP* 3.6 12.6 - - + -
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASN 2.9 21.8 + - - +
88A LEU* 3.1 12.1 + - - +
90A THR* 1.3 78.5 - - - +
92A TYR* 1.3 62.8 + - - +
94A ILE* 4.9 2.9 - - - -
95A LYS* 2.9 31.9 + - + +
98A TRP* 5.5 0.9 - - + -
99A PRO* 4.0 22.2 - - + -
100A LEU* 4.5 11.0 - - + -
1203A OLA 3.8 49.1 - - + -
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU 3.0 11.8 + - - +
89A TYR* 3.3 22.2 - + + +
91A VAL* 1.3 76.9 - - - +
93A ILE* 1.3 62.5 + - - +
96A GLY* 3.2 19.9 + - - -
97A TYR* 3.4 37.0 + - - -
98A TRP* 3.5 24.4 - + + -
108A TRP* 4.1 15.7 - + - -
184A GLN* 2.6 25.9 + - - +
185A CYS* 3.1 41.9 + - + -
186A PHE* 5.6 0.5 - - - -
1205A P6G 4.7 8.7 - - - -
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Residues in contact with ILE 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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32A MET* 4.1 8.0 - - + +
35A ILE* 4.0 34.5 - - + -
39A THR* 5.8 1.6 - - + -
89A TYR* 2.9 57.3 + - + +
90A THR* 3.8 9.9 - - + +
91A VAL 3.3 0.2 - - - -
92A TYR* 1.3 76.4 - - - +
94A ILE* 1.3 64.5 + - + +
96A GLY* 3.3 12.1 + - - -
436A SER* 5.1 10.8 - - - +
440A TRP* 5.0 9.9 - - + -
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Residues in contact with ILE 94 (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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28A GLU* 4.5 3.5 - - - +
32A MET* 3.6 51.0 - - + +
35A ILE* 4.3 13.9 - - + -
36A ALA* 3.9 32.3 - - + -
90A THR* 2.9 30.1 + - - +
91A VAL* 4.2 3.4 - - - +
93A ILE* 1.3 73.9 - - - +
95A LYS* 1.3 62.8 + - - +
96A GLY* 3.3 0.5 + - - -
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Residues in contact with LYS 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 VAL* 2.9 21.3 + - + +
94A ILE* 1.3 79.5 - - - +
96A GLY* 1.3 56.4 + - - +
97A TYR* 3.1 43.8 - - + +
99A PRO* 4.3 15.7 - - + -
1203A OLA 6.1 0.9 - - - +
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Residues in contact with GLY 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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32A MET* 6.1 0.4 - - - -
92A TYR* 3.2 13.2 + - - -
93A ILE 3.3 7.6 + - - -
94A ILE 3.2 3.8 - - - -
95A LYS* 1.3 77.6 - - - +
97A TYR* 1.3 62.9 + - - +
184A GLN* 4.9 5.0 + - - +
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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