Contacts of the helix formed by residues 92 - 105 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88F GLU 3.1 12.5 + - - +
89F MET 3.2 13.0 - - - +
90F LEU 3.1 1.7 - - - -
91F LYS* 1.3 71.6 - - - +
93F GLU* 1.3 62.7 + - - +
94F VAL* 3.1 13.0 + - - +
95F ARG* 3.0 25.3 + - + +
96F THR* 3.0 26.0 + - - -
332F TYR* 4.1 9.7 - - + +
333F THR* 3.4 13.8 - - - -
334F HIS* 3.0 46.4 + - + +
335F TRP* 4.0 0.3 - - - -
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Residues in contact with GLU 93 (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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243E TYR* 3.5 21.5 - - + +
91F LYS* 2.9 17.2 + - - +
92F ASP* 1.3 69.6 + - - +
94F VAL* 1.3 61.8 + - + +
97F LEU* 2.8 54.8 + - + +
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Residues in contact with VAL 94 (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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92F ASP* 3.1 7.9 + - - +
93F GLU* 1.3 78.0 - - + +
95F ARG* 1.3 62.2 + - - +
97F LEU* 4.6 0.6 - - - +
98F THR* 2.7 33.6 + - - +
324F PHE* 3.5 31.2 - - + -
325F SER 5.0 1.8 - - - +
331F PRO* 4.4 23.6 - - + +
332F TYR 3.6 20.6 - - - +
333F THR* 4.2 12.6 - - + -
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Residues in contact with ARG 95 (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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89F MET* 3.1 32.2 + - - +
90F LEU* 4.1 5.5 - - - +
92F ASP* 3.0 18.8 + - - +
94F VAL* 1.3 82.7 - - - +
96F THR* 1.3 88.5 + - - +
98F THR* 3.6 1.6 - - - -
99F TYR* 3.1 41.9 + - + -
124F ILE* 4.7 1.2 - - - +
125F LEU* 5.6 1.8 - - - +
185F GLU* 3.0 33.3 - - - +
324F PHE* 4.2 10.5 - - + -
333F THR* 5.6 0.2 - - - +
334F HIS* 3.6 14.8 - - - -
335F TRP* 3.5 34.3 - - + -
401F SAH 3.0 30.3 + - - -
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Residues in contact with THR 96 (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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243E TYR* 3.2 43.7 - - + -
89F MET 3.2 7.4 + - - -
90F LEU* 3.3 6.2 + - + -
92F ASP 3.0 11.1 + - - -
95F ARG* 1.3 104.4 + - - +
97F LEU* 1.3 58.0 + - - +
99F TYR* 3.4 6.4 + - - +
100F ARG* 2.9 26.4 + - - +
124F ILE* 4.5 7.0 - - + -
125F LEU* 5.7 1.6 - - + -
128F PHE* 3.8 17.7 - - + -
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Residues in contact with LEU 97 (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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243E TYR* 3.9 24.9 - - + -
93F GLU* 2.8 46.2 + - + +
94F VAL* 5.1 0.9 - - - -
96F THR* 1.3 71.8 - - - +
98F THR* 1.3 58.2 + - - +
100F ARG* 3.2 38.7 + - - +
101F ASN* 2.8 42.3 + - - +
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Residues in contact with THR 98 (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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94F VAL* 2.7 24.6 + - - +
95F ARG 3.2 4.1 + - - -
97F LEU* 1.3 77.4 - - - +
99F TYR* 1.3 56.6 + - - +
101F ASN* 3.2 6.0 + - - +
102F SER* 2.8 28.9 + - - -
315F PHE* 3.5 27.8 - - + -
322F MET* 3.8 9.8 - - + +
323F GLY 3.8 32.7 + - - +
324F PHE* 3.8 14.7 - - + +
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Residues in contact with TYR 99 (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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95F ARG* 3.1 37.5 + - + -
96F THR* 3.7 8.7 - - - +
98F THR* 1.3 74.2 - - - +
100F ARG* 1.3 64.2 + - - +
102F SER* 2.7 22.9 + - - -
103F MET* 3.4 21.4 + - + +
125F LEU* 3.8 35.4 - - + -
128F PHE* 4.4 2.0 - - + -
183F ILE* 5.6 0.2 - - + -
184F SER 2.7 34.9 + - - -
185F GLU* 3.1 22.9 - - + -
187F MET* 3.3 22.4 - - + +
215F PHE* 4.0 4.7 - - + -
216F PRO* 3.3 6.6 - - + +
315F PHE* 3.9 30.3 - + - -
324F PHE* 4.5 5.6 - + - -
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Residues in contact with ARG 100 (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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243E TYR* 4.5 23.0 + - - +
96F THR 2.9 13.2 + - - +
97F LEU* 3.5 31.9 - - + +
98F THR 3.2 0.2 - - - -
99F TYR* 1.3 75.7 - - - +
101F ASN* 1.3 75.9 + - - +
103F MET* 3.2 2.8 + - - +
104F TYR* 2.8 59.8 + - + +
128F PHE* 3.4 52.7 - - + -
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Residues in contact with ASN 101 (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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97F LEU* 2.8 27.0 + - - +
98F THR* 3.7 1.0 - - - +
100F ARG* 1.3 102.5 - - - +
102F SER* 1.3 64.4 + - - +
104F TYR* 4.7 1.6 - - - +
105F HIS* 3.0 64.2 + - + +
106F ASN* 4.0 0.5 - - - +
322F MET* 3.7 22.8 - - - +
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Residues in contact with SER 102 (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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98F THR 2.8 14.8 + - - -
99F TYR* 2.7 22.9 + - - -
101F ASN* 1.3 76.4 - - - +
103F MET* 1.3 60.4 + - - +
106F ASN* 2.9 22.2 - - - +
215F PHE* 3.3 29.7 - - - -
315F PHE* 3.7 28.4 - - - -
318F CYS* 3.8 11.9 - - - -
322F MET* 3.6 10.3 - - - -
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Residues in contact with MET 103 (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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99F TYR* 3.5 23.6 - - + +
100F ARG 3.2 4.4 + - - +
101F ASN 3.0 0.4 - - - -
102F SER* 1.3 82.4 - - - +
104F TYR* 1.3 64.2 + - + +
105F HIS 3.4 0.2 - - - -
106F ASN 2.9 29.1 + - - +
107F LYS 3.4 1.6 + - - -
110F PHE* 3.7 29.3 - - + -
125F LEU* 3.9 21.5 - - + +
128F PHE* 3.9 9.2 - - + +
129F ALA* 3.6 33.9 - - - -
132F ALA* 3.8 18.2 - - + +
183F ILE* 3.8 31.0 - - + -
215F PHE* 4.6 2.0 - - + -
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Residues in contact with TYR 104 (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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243E TYR 5.0 1.0 + - - -
245E PHE* 3.5 22.0 - - - -
100F ARG* 2.8 58.1 + - + +
101F ASN* 4.7 1.1 - - - +
103F MET* 1.3 74.6 - - + +
105F HIS* 1.3 62.4 + - + +
106F ASN 3.1 0.9 + - - -
107F LYS* 3.1 31.7 + - - +
128F PHE* 3.4 37.5 - - - -
131F LYS* 3.4 25.7 - - + +
132F ALA* 4.5 5.4 - - + -
345H TYR* 2.6 25.3 + - - -
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Residues in contact with HIS 105 (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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101F ASN* 3.0 56.5 + - + +
104F TYR* 1.3 83.4 - - + +
106F ASN* 1.3 63.1 + - - +
107F LYS 3.8 0.9 - - - -
108F HIS* 4.8 0.5 + - - -
322F MET* 4.8 9.0 - - + +
229H ARG* 4.7 26.3 + - - -
303H TYR* 2.5 48.9 + + + +
345H TYR* 3.6 12.9 - + - -
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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