Contacts of the helix formed by residues 85 - 93 (chain C) in PDB entry 3SPD
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 HIS 85 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C HIS 3.7 3.2 + - - -
84C VAL* 1.3 76.4 - - - +
86C PRO* 1.3 82.9 - - + +
87C LEU* 3.0 41.6 + - + +
88C GLU* 2.9 18.2 + - + +
89C ILE* 2.9 18.7 + - - +
139C ALA 3.0 23.9 + - - -
141C PRO* 4.0 3.6 - - + +
187C ARG* 3.3 48.7 + - - +
702C SO4 2.9 24.6 + - - -
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Residues in contact with PRO 86 (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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84C VAL 3.6 3.3 - - - +
85C HIS* 1.3 101.0 - - + +
87C LEU* 1.3 57.3 + - + +
89C ILE* 3.2 4.6 + - + +
90C MET* 2.9 35.4 + - - +
137C PHE* 3.6 35.8 - - + -
138C HIS 3.5 20.6 - - - +
141C PRO* 3.5 20.2 - - + -
146C LEU* 3.7 17.9 - - + -
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Residues in contact with LEU 87 (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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85C HIS* 3.0 21.6 + - + +
86C PRO* 1.3 78.5 - - + +
88C GLU* 1.3 58.6 + - + +
90C MET* 3.4 4.4 + - + +
91C MET* 3.0 43.6 + - + +
139C ALA* 4.0 16.2 - - + +
175C VAL* 4.1 17.9 - - + -
184C LEU* 4.2 13.1 - - + +
185C PRO* 3.5 36.8 - - + +
186C THR 4.0 1.3 - - - +
187C ARG* 3.5 43.5 - - + +
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Residues in contact with GLU 88 (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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84C VAL* 3.6 14.4 - - + -
85C HIS* 2.9 25.2 + - + +
87C LEU* 1.3 74.6 - - + +
89C ILE* 1.3 61.8 + - - +
91C MET* 3.4 26.1 - - - +
92C LYS* 2.9 57.4 + - + +
93C HIS* 3.5 10.8 - - + -
187C ARG* 5.4 4.9 - - - +
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Residues in contact with ILE 89 (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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81C LEU* 4.2 7.6 - - + +
84C VAL* 3.5 26.5 - - + +
85C HIS 2.9 16.8 + - - +
86C PRO* 3.4 10.1 - - + +
88C GLU* 1.3 77.7 - - - +
90C MET* 1.3 63.2 + - - +
93C HIS* 3.0 44.1 + - + +
96C LEU* 3.9 31.9 - - + -
97C VAL* 3.7 17.2 - - + +
100C LEU* 5.4 0.4 - - + -
137C PHE* 4.5 11.9 - - + -
146C LEU* 3.9 25.8 - - + -
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Residues in contact with MET 90 (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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86C PRO 2.9 23.0 + - - +
87C LEU* 3.6 7.4 - - - +
89C ILE* 1.3 76.3 - - - +
91C MET* 1.3 60.3 + - - +
94C ARG* 2.8 36.8 + - - +
97C VAL* 4.2 7.9 - - - -
137C PHE* 3.9 17.5 - - + -
175C VAL* 4.3 7.9 - - + -
176C LYS 3.7 15.9 - - - +
177C ILE* 3.6 45.8 - - - +
179C THR 3.9 17.0 - - - +
181C THR* 3.5 4.5 + - - -
184C LEU* 3.6 29.4 - - + -
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Residues in contact with MET 91 (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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87C LEU* 3.0 27.0 + - + +
88C GLU* 3.4 26.7 - - - +
89C ILE 3.2 0.2 - - - -
90C MET* 1.3 79.5 - - - +
92C LYS* 1.3 76.3 + - + +
93C HIS 3.8 0.2 - - - -
94C ARG* 4.4 9.0 - - - +
181C THR* 4.0 21.5 + - + +
184C LEU* 3.6 23.1 - - + -
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Residues in contact with LYS 92 (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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88C GLU* 2.9 44.1 + - + +
91C MET* 1.3 97.0 - - + +
93C HIS* 1.3 76.4 + - + +
94C ARG* 3.7 4.7 + - - -
703C SO4 5.0 2.3 + - - -
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Residues in contact with HIS 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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80C HIS* 4.9 8.0 + + - -
81C LEU* 3.6 16.5 - - + +
84C VAL* 4.1 14.9 - - + +
88C GLU* 3.5 19.7 - - + +
89C ILE* 3.0 38.1 + - + +
91C MET 3.8 0.2 - - - -
92C LYS* 1.3 91.6 + - + +
94C ARG* 1.3 64.2 + - - +
96C LEU* 3.1 13.1 + - + +
97C VAL* 3.2 14.0 + - - +
703C SO4 2.7 38.8 + - - +
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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