Contacts of the helix formed by residues 92 - 105 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C GLU 3.3 11.3 + - - +
89C MET 3.3 13.5 - - - +
90C LEU 3.9 0.7 - - - -
91C LYS* 1.3 73.0 - - - +
93C GLU* 1.3 62.5 + - - +
94C VAL* 3.3 11.4 + - - +
95C ARG* 3.0 27.2 + - + +
96C THR* 3.0 25.5 + - - -
332C TYR* 4.2 9.3 - - + +
333C THR* 3.5 12.4 - - - -
334C HIS* 2.8 46.3 + - + +
335C TRP* 4.1 0.2 - - - -
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Residues in contact with GLU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LYS* 3.0 17.4 + - - +
92C ASP* 1.3 69.4 + - - +
94C VAL* 1.3 60.8 + - + +
97C LEU* 2.7 58.5 + - + +
243D TYR* 3.7 20.6 - - + +
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ASP* 3.3 7.3 + - - +
93C GLU* 1.3 77.3 - - + +
95C ARG* 1.3 61.4 + - - +
97C LEU* 5.2 0.4 - - - -
98C THR* 2.7 34.2 + - - +
324C PHE* 3.5 31.6 - - + -
325C SER 5.2 1.3 - - - +
331C PRO* 4.4 23.8 - - + +
332C TYR 3.6 21.1 - - - +
333C THR* 4.1 12.3 - - + -
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Residues in contact with ARG 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C MET* 2.9 37.8 + - - +
90C LEU* 4.1 7.9 - - - +
92C ASP* 3.0 22.6 + - - +
94C VAL* 1.3 80.4 - - - +
96C THR* 1.3 83.9 + - - +
98C THR* 3.7 2.1 - - - -
99C TYR* 3.1 41.3 + - + -
124C ILE* 4.7 1.2 - - - +
125C LEU* 5.6 2.9 - - - +
185C GLU* 3.0 24.9 - - - +
324C PHE* 4.4 10.1 - - + -
334C HIS* 3.6 14.6 - - - -
335C TRP* 3.5 35.4 - - + -
401C SAH 2.8 38.2 + - - -
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Residues in contact with THR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C MET 3.2 16.3 + - - -
90C LEU* 3.3 6.6 + - + -
92C ASP 3.0 16.3 + - - -
95C ARG* 1.3 90.9 + - - +
97C LEU* 1.3 67.0 + - - +
99C TYR* 3.1 6.6 + - + +
100C ARG* 2.9 21.5 + - - +
124C ILE* 4.6 6.5 - - + -
125C LEU* 5.7 1.1 - - + -
128C PHE* 3.9 19.3 - - + -
243D TYR* 3.4 37.9 - - + -
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Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C GLU* 2.7 46.6 + - + +
94C VAL* 4.7 0.9 - - - +
96C THR* 1.3 73.4 - - - +
98C THR* 1.3 55.6 + - - +
100C ARG* 3.5 39.5 - - - +
101C ASN* 2.8 41.6 + - - +
243D TYR* 3.9 24.0 - - + -
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Residues in contact with THR 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C VAL* 2.7 26.9 + - - +
95C ARG 3.7 3.4 - - - -
97C LEU* 1.3 77.0 - - - +
99C TYR* 1.3 62.3 + - - +
101C ASN* 3.8 5.8 - - - +
102C SER* 2.9 22.3 + - - -
315C PHE* 3.5 27.6 - - + -
322C MET* 3.9 9.7 - - + +
323C GLY 4.0 24.3 + - - +
324C PHE* 3.8 21.3 - - + +
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Residues in contact with TYR 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ARG* 3.1 36.6 + - + +
96C THR* 3.1 10.3 + - - +
98C THR* 1.3 76.2 - - - +
100C ARG* 1.3 61.2 + - - +
102C SER* 2.8 22.2 + - - -
103C MET* 3.5 21.2 - - + +
125C LEU* 3.8 35.2 - - + -
128C PHE* 4.4 1.3 - - - -
183C ILE* 5.7 0.4 - - + -
184C SER 2.8 33.1 + - - -
185C GLU* 3.3 22.7 - - + -
187C MET* 3.3 23.4 - - + +
215C PHE* 3.8 14.8 - - + -
216C PRO* 3.4 5.4 - - - +
315C PHE* 3.9 27.4 - + - -
324C PHE* 4.5 5.8 - + - -
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C THR 2.9 11.6 + - - +
97C LEU* 3.5 33.2 - - - +
99C TYR* 1.3 78.9 - - - +
101C ASN* 1.3 75.6 + - - +
103C MET* 3.1 2.8 + - - +
104C TYR* 2.9 61.9 + - + +
128C PHE* 3.4 48.9 - - + -
243D TYR* 4.6 20.9 + - - +
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Residues in contact with ASN 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LEU* 2.8 27.4 + - - +
98C THR* 4.5 1.1 - - - -
100C ARG* 1.3 99.2 - - - +
102C SER* 1.3 68.3 + - - +
104C TYR* 4.7 1.0 - - - +
105C HIS* 2.9 65.3 + - + +
322C MET* 3.7 24.2 - - + +
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C THR 2.9 14.3 + - - -
99C TYR* 2.8 19.6 + - - -
101C ASN* 1.3 77.2 - - - +
103C MET* 1.3 60.7 + - - +
106C ASN* 2.8 25.2 - - - +
215C PHE* 3.4 24.1 - - - -
315C PHE* 3.7 29.8 - - - -
318C CYS* 3.8 14.1 - - - -
322C MET* 3.6 10.2 - - - -
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Residues in contact with MET 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C TYR* 3.5 24.2 - - + +
100C ARG 3.1 4.1 + - - +
101C ASN 3.0 0.6 - - - -
102C SER* 1.3 81.4 - - - +
104C TYR* 1.3 64.7 + - + +
105C HIS 3.2 1.3 - - - -
106C ASN 2.9 28.9 + - - +
107C LYS 3.3 1.9 + - - -
110C PHE* 3.7 28.9 - - + -
125C LEU* 3.8 29.2 - - + +
128C PHE* 3.7 8.7 - - + -
129C ALA* 3.5 33.0 - - - -
132C ALA* 3.8 19.0 - - + +
183C ILE* 3.9 23.6 - - + -
215C PHE* 4.7 1.8 - - + -
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Residues in contact with TYR 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A TYR* 2.6 23.4 + - - -
100C ARG* 2.9 58.5 + - + +
101C ASN* 4.7 0.7 - - - +
103C MET* 1.3 75.8 - - + +
105C HIS* 1.3 62.7 + - + +
106C ASN 3.2 0.8 + - - -
107C LYS* 3.1 34.3 + - - +
128C PHE* 3.4 46.3 - - - -
131C LYS* 3.5 27.2 - - + +
132C ALA* 4.6 4.5 - - + -
243D TYR 5.0 1.2 + - - -
245D PHE* 3.8 8.8 - - - -
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Residues in contact with HIS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ARG* 4.7 25.4 + - - -
303A TYR* 2.7 48.6 + + + +
345A TYR* 3.3 16.7 + + + -
347A THR* 5.2 0.3 + - - -
101C ASN* 2.9 55.1 + - + +
104C TYR* 1.3 83.3 - - + +
106C ASN* 1.3 63.3 + - - +
107C LYS 3.8 0.4 - - - -
108C HIS* 4.8 0.9 + - - -
322C MET* 4.8 10.2 - - + +
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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