Contacts of the helix formed by residues 92 - 105 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88L GLU 3.2 12.3 + - - +
89L MET 3.3 12.3 - - - +
90L LEU 3.1 2.1 - - - -
91L LYS* 1.3 73.5 - - - +
93L GLU* 1.3 56.3 + - - +
94L VAL* 3.2 12.1 + - - +
95L ARG* 3.1 25.0 + - + +
96L THR* 3.0 30.0 + - - -
332L TYR* 4.0 10.3 - - + +
333L THR* 3.5 13.0 - - - -
334L HIS* 2.9 48.1 + - + +
335L TRP* 3.9 0.5 - - - -
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Residues in contact with GLU 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K TYR* 3.4 23.6 - - + +
91L LYS* 2.8 17.4 + - - +
92L ASP* 1.3 68.8 + - - +
94L VAL* 1.3 60.7 + - + +
97L LEU* 2.7 56.2 + - + +
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Residues in contact with VAL 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92L ASP* 3.2 7.9 + - - +
93L GLU* 1.3 78.4 - - + +
95L ARG* 1.3 65.0 + - - +
97L LEU* 4.6 1.1 - - - +
98L THR* 2.8 30.0 + - - +
324L PHE* 3.5 31.2 - - + -
325L SER 5.1 2.0 - - - +
331L PRO* 4.4 24.0 - - + +
332L TYR 3.6 20.6 - - - +
333L THR* 4.1 13.0 - - + -
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Residues in contact with ARG 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L MET* 2.9 38.1 + - - +
90L LEU* 4.0 8.7 - - - +
92L ASP* 3.1 19.3 + - - +
94L VAL* 1.3 84.2 - - - +
96L THR* 1.3 86.1 + - - +
98L THR* 3.6 1.9 - - - -
99L TYR* 3.0 40.5 + - + -
124L ILE* 4.7 1.6 - - - +
125L LEU* 5.5 2.1 - - - +
185L GLU* 3.0 25.8 + - - +
324L PHE* 4.4 11.4 - - + -
334L HIS* 3.6 15.5 - - - -
335L TRP* 3.5 33.9 - - + -
401L SAH 2.9 37.0 + - - -
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Residues in contact with THR 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K TYR* 3.3 42.0 - - + -
89L MET 3.1 17.2 + - - -
90L LEU* 3.3 5.9 + - + -
92L ASP 3.0 11.2 + - - -
95L ARG* 1.3 92.1 + - - +
97L LEU* 1.3 64.4 + - - +
99L TYR* 3.2 7.5 + - - +
100L ARG* 2.9 20.8 + - - +
124L ILE* 4.5 7.4 - - + -
125L LEU* 5.6 1.3 - - + -
128L PHE* 3.8 18.6 - - + -
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Residues in contact with LEU 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K TYR* 3.7 25.1 - - + -
93L GLU* 2.7 46.3 + - + +
94L VAL* 4.6 1.1 - - - +
96L THR* 1.3 73.5 - - - +
98L THR* 1.3 55.7 + - - +
100L ARG* 3.5 38.5 - - - +
101L ASN* 2.8 41.6 + - - +
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Residues in contact with THR 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L VAL* 2.8 25.3 + - - +
95L ARG 3.6 3.4 - - - -
97L LEU* 1.3 79.7 - - - +
99L TYR* 1.3 64.2 + - - +
101L ASN* 3.7 5.3 - - - +
102L SER* 2.9 22.4 + - - -
315L PHE* 3.5 30.5 - - + -
322L MET* 3.9 11.3 - - + +
323L GLY 3.9 23.5 + - - +
324L PHE* 3.9 18.6 - - + +
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Residues in contact with TYR 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95L ARG* 3.0 37.9 + - + +
96L THR* 3.2 9.2 + - - +
98L THR* 1.3 76.2 - - - +
100L ARG* 1.3 60.5 + - - +
102L SER* 2.6 23.0 + - - -
103L MET* 3.4 21.1 - - + +
125L LEU* 3.8 34.1 - - + -
128L PHE* 4.3 1.6 - - - -
183L ILE* 5.5 0.4 - - + -
184L SER 2.6 35.6 + - - -
185L GLU* 3.2 23.9 - - + +
187L MET* 3.4 18.3 - - + +
215L PHE* 4.1 7.4 - - + -
216L PRO* 3.4 9.2 - - - +
315L PHE* 4.0 31.4 - + - -
324L PHE* 4.6 6.1 - + - -
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Residues in contact with ARG 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K TYR* 4.3 24.9 + - - +
96L THR 2.9 12.4 + - - +
97L LEU* 3.5 31.1 - - + +
99L TYR* 1.3 77.9 - - - +
101L ASN* 1.3 75.2 + - - +
103L MET* 3.1 3.3 + - - +
104L TYR* 2.9 61.4 + - + +
128L PHE* 3.5 49.1 - - + -
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Residues in contact with ASN 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97L LEU* 2.8 27.1 + - - +
98L THR* 4.6 0.9 - - - -
100L ARG* 1.3 102.4 - - - +
102L SER* 1.3 63.6 + - - +
104L TYR* 4.6 1.4 - - - +
105L HIS* 2.9 64.6 + - + +
322L MET* 3.7 24.2 - - + +
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Residues in contact with SER 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98L THR 2.9 15.9 + - - -
99L TYR* 2.6 22.7 + - - -
101L ASN* 1.3 76.4 - - - +
103L MET* 1.3 65.9 + - - +
106L ASN* 2.9 21.2 - - - +
215L PHE* 3.4 24.5 - - - -
315L PHE* 3.8 28.3 - - - -
318L CYS* 3.7 10.3 - - - -
322L MET* 3.6 10.5 - - - -
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Residues in contact with MET 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L TYR* 3.4 20.2 - - + +
100L ARG 3.1 4.4 + - - +
101L ASN 3.0 0.2 - - - -
102L SER* 1.3 86.7 - - - +
104L TYR* 1.3 62.2 - - + +
105L HIS 3.3 1.1 - - - -
106L ASN 2.8 32.9 + - - +
107L LYS* 3.2 4.3 + - - -
110L PHE* 3.6 30.7 - - + -
125L LEU* 3.9 17.0 - - + +
128L PHE* 3.8 11.9 - - + -
129L ALA* 3.6 31.6 - - - -
132L ALA* 3.9 14.5 - - + +
183L ILE* 3.9 31.9 - - + -
215L PHE* 4.6 1.8 - - + -
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Residues in contact with TYR 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K TYR 4.8 1.9 + - - -
245K PHE* 3.5 29.1 - - - -
100L ARG* 2.9 52.7 + - + +
101L ASN* 4.6 1.1 - - - +
103L MET* 1.3 79.3 - - + +
105L HIS* 1.3 62.3 + - + +
106L ASN 3.4 0.7 + - - -
107L LYS* 3.1 32.5 + - - +
128L PHE* 3.3 37.9 - - - -
131L LYS* 3.5 19.3 - - + +
132L ALA* 4.5 5.2 - - + -
345N TYR* 2.7 24.3 + - - -
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Residues in contact with HIS 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L ASN* 2.9 56.4 + - + +
104L TYR* 1.3 81.8 - - + +
106L ASN* 1.3 61.6 + - - +
107L LYS 3.8 0.9 - - - -
108L HIS* 4.8 0.9 + - - -
322L MET* 4.7 10.3 - - + +
229N ARG* 4.9 22.8 + - - -
303N TYR* 2.5 49.7 + + + +
345N TYR* 3.7 12.8 + + - -
347N THR* 5.2 0.5 + - - +
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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