Contacts of the helix formed by residues 92 - 105 (chain B) in PDB entry 5DST
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 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B GLU 3.2 11.7 + - - +
89B MET 3.4 11.7 - - - +
90B LEU 3.2 1.5 - - - -
91B LYS* 1.3 72.5 - - - +
93B GLU* 1.3 62.3 + - - +
94B VAL* 3.1 12.3 + - - +
95B ARG* 3.1 25.5 + - + +
96B THR* 3.1 24.3 + - - -
332B TYR* 4.1 10.6 - - + +
333B THR* 3.5 13.4 - - - -
334B HIS* 2.9 46.4 + - + +
335B TRP* 4.0 0.3 - - - -
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Residues in contact with GLU 93 (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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243A TYR* 3.4 24.5 - - + +
91B LYS 2.8 16.9 + - - +
92B ASP* 1.3 69.0 + - - +
94B VAL* 1.3 61.0 + - + +
97B LEU* 2.8 55.5 + - + +
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Residues in contact with VAL 94 (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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92B ASP* 3.1 7.9 + - - +
93B GLU* 1.3 77.2 - - + +
95B ARG* 1.3 63.3 + - - +
97B LEU* 5.2 0.4 - - - -
98B THR* 2.8 32.7 + - - +
324B PHE* 3.6 30.7 - - + -
325B SER 5.1 1.8 - - - +
331B PRO* 4.4 24.2 - - + +
332B TYR 3.7 20.4 - - - +
333B THR* 4.2 12.8 - - + -
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Residues in contact with ARG 95 (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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89B MET* 3.0 35.4 + - - +
90B LEU* 4.2 5.9 - - - +
92B ASP* 3.1 20.0 + - - +
94B VAL* 1.3 84.6 - - - +
96B THR* 1.3 87.7 + - - +
98B THR* 3.7 1.7 - - - -
99B TYR* 3.2 39.9 + - + -
124B ILE* 4.6 2.0 - - - +
125B LEU* 5.4 2.5 - - - +
185B GLU* 3.1 24.4 + - - +
324B PHE* 4.4 10.3 - - + -
334B HIS* 3.6 15.3 - - - -
335B TRP* 3.6 33.2 - - + -
401B SAH 2.7 40.6 + - - -
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Residues in contact with THR 96 (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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243A TYR* 3.2 42.2 - - + -
89B MET 3.3 10.4 + - - -
90B LEU* 3.1 18.7 + - + -
92B ASP 3.1 6.7 + - - -
95B ARG* 1.3 94.4 + - - +
97B LEU* 1.3 59.1 + - - +
99B TYR* 3.4 6.8 + - - +
100B ARG* 2.9 26.2 + - - +
124B ILE* 4.5 7.0 - - + -
125B LEU* 5.7 1.1 - - + -
128B PHE* 3.7 18.3 - - + -
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Residues in contact with LEU 97 (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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243A TYR* 3.9 24.2 - - + -
93B GLU* 2.8 44.4 + - + +
94B VAL* 4.6 0.7 - - - +
96B THR* 1.3 71.6 - - - +
98B THR* 1.3 60.7 + - - +
100B ARG* 3.4 39.4 - - - +
101B ASN* 2.8 41.2 + - - +
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Residues in contact with THR 98 (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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94B VAL* 2.8 25.2 + - - +
95B ARG 3.7 3.1 - - - -
96B THR 3.3 0.2 - - - -
97B LEU* 1.3 78.2 - - - +
99B TYR* 1.3 64.0 + - - +
101B ASN* 3.2 7.0 + - - +
102B SER* 2.9 21.7 + - - -
315B PHE* 3.5 27.8 - - + -
322B MET* 3.8 10.4 - - + +
323B GLY 4.0 24.4 + - - +
324B PHE* 3.8 20.9 - - + +
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Residues in contact with TYR 99 (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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95B ARG* 3.2 36.0 + - + +
96B THR* 3.6 8.5 - - - +
98B THR* 1.3 78.0 - - - +
100B ARG* 1.3 61.7 + - - +
102B SER* 2.6 23.0 + - - -
103B MET* 3.4 20.6 - - + +
125B LEU* 3.8 34.1 - - + -
128B PHE* 4.4 1.3 - - - -
183B ILE* 5.6 0.4 - - + -
184B SER 2.7 34.0 + - - -
185B GLU* 3.2 22.6 - - + -
187B MET* 3.4 19.0 - - + +
215B PHE* 4.0 4.9 - - + -
216B PRO* 3.3 15.4 - - + +
315B PHE* 4.0 27.8 - + - -
324B PHE* 4.5 6.1 - + - -
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Residues in contact with ARG 100 (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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243A TYR* 4.4 21.9 + - - +
96B THR 2.9 14.1 + - - +
97B LEU* 3.4 33.1 - - + +
98B THR 3.2 0.4 - - - -
99B TYR* 1.3 77.9 - - - +
101B ASN* 1.3 73.6 + - - +
103B MET* 3.1 5.0 + - - +
104B TYR* 2.8 60.2 + - + +
128B PHE* 3.4 49.8 - - + -
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Residues in contact with ASN 101 (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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97B LEU* 2.8 30.8 + - - +
98B THR* 3.7 4.9 - - - +
100B ARG* 1.3 97.2 - - - +
102B SER* 1.3 63.3 + - - +
104B TYR* 4.4 2.1 - - - +
105B HIS* 2.8 64.6 + - + +
322B MET* 3.8 21.3 - - + +
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Residues in contact with SER 102 (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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98B THR 2.9 14.3 + - - -
99B TYR* 2.6 24.1 + - - -
101B ASN* 1.3 76.9 - - - +
103B MET* 1.3 64.8 + - - +
106B ASN* 2.7 27.9 - - - +
215B PHE* 3.5 18.3 - - - -
315B PHE* 3.8 27.6 - - - -
318B CYS* 3.9 13.2 - - - -
322B MET* 3.6 10.7 - - - -
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Residues in contact with MET 103 (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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99B TYR* 3.4 25.4 - - + +
100B ARG 3.1 4.4 + - - +
101B ASN 3.0 0.2 - - - -
102B SER* 1.3 82.2 - - - +
104B TYR* 1.3 64.8 + - + +
105B HIS 3.3 0.2 - - - -
106B ASN 3.0 26.7 + - - +
107B LYS 3.4 1.7 + - - -
110B PHE* 3.7 31.6 - - + -
125B LEU* 3.9 28.9 - - + +
128B PHE* 3.8 9.0 - - + +
129B ALA* 3.7 30.1 - - - -
132B ALA* 3.7 19.2 - - + +
183B ILE* 3.9 24.0 - - + -
215B PHE* 4.7 2.5 - - + -
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Residues in contact with TYR 104 (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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243A TYR 5.0 1.3 + - - -
245A PHE* 3.7 21.3 - - - -
100B ARG* 2.8 57.0 + - + +
101B ASN* 4.6 1.1 - - - +
103B MET* 1.3 74.0 - - + +
105B HIS* 1.3 61.5 + - + +
106B ASN 3.2 0.7 + - - -
107B LYS* 3.1 32.8 + - - +
128B PHE* 3.4 36.0 - - - -
131B LYS* 3.5 25.3 - - + +
132B ALA* 4.6 5.2 - - + -
345D TYR* 2.6 24.8 + - - -
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Residues in contact with HIS 105 (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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101B ASN* 2.8 58.7 + - + +
104B TYR* 1.3 79.3 - - + +
106B ASN* 1.3 61.6 + - - +
107B LYS 3.7 1.7 + - - -
108B HIS* 4.8 1.0 + - - -
322B MET* 5.0 8.4 - - + +
229D ARG* 4.4 29.7 + - - -
303D TYR* 2.5 51.4 + + + +
345D TYR* 3.5 13.1 + + - -
347D THR* 5.2 0.2 + - - -
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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