Contacts of the helix formed by residues 698 - 710 (chain C) in PDB entry 5OEO
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 698 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A MET* 4.1 9.6 - - - +
127A GLU* 6.0 1.3 - - - +
696C SER 3.9 1.6 + - - -
697C SER* 1.3 77.3 + - - +
699C ARG* 1.3 68.3 + - + +
700C GLY 3.1 1.0 + - - -
701C TRP* 3.2 9.4 + - + +
702C GLU* 3.0 49.0 + - - +
705C ARG* 5.4 0.3 + - - -
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Residues in contact with ARG 699 (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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114A GLU* 5.1 11.8 + - - -
116A LEU* 5.4 12.8 - - + -
120A GLU* 5.9 0.4 - - - +
697C SER* 2.9 19.9 + - - +
698C HIS* 1.3 83.4 - - + +
700C GLY* 1.3 56.0 + - - +
702C GLU* 3.8 18.4 - - + +
703C ILE* 2.8 44.2 + - + +
706C GLN* 6.1 1.3 - - - +
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Residues in contact with GLY 700 (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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105A LEU* 4.9 10.6 - - - +
116A LEU* 4.0 27.9 - - - +
120A GLU* 5.3 2.8 + - - -
124A MET* 3.9 15.3 - - - -
697C SER* 3.2 7.4 + - - -
698C HIS 3.1 1.6 - - - -
699C ARG* 1.3 79.2 - - - +
701C TRP* 1.3 60.3 + - - +
703C ILE* 3.6 14.3 - - - +
704C LEU* 4.2 6.4 + - - +
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Residues in contact with TRP 701 (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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100A ILE* 3.4 45.3 - - + -
105A LEU* 3.5 31.9 - - + -
124A MET* 3.2 69.2 + - + +
125A ILE* 4.1 7.2 - - + -
127A GLU* 4.8 3.1 - - - -
128A ALA* 3.6 11.5 - - + +
136A VAL* 4.5 4.5 - - + -
141A PHE* 4.1 11.9 - + - -
144A MET* 3.3 30.5 - - + -
698C HIS* 3.2 8.7 + - + +
700C GLY* 1.3 75.2 - - - +
702C GLU* 1.3 64.6 + - - +
703C ILE 3.3 0.4 - - - -
704C LEU* 3.5 7.9 + - + +
705C ARG* 3.3 44.7 + - - +
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Residues in contact with GLU 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A MET* 5.3 9.6 - - + +
698C HIS* 3.0 44.7 + - - +
699C ARG* 3.1 13.8 + - + +
701C TRP* 1.3 76.8 - - - +
703C ILE* 1.3 66.2 + - - +
705C ARG* 3.3 11.6 + - - +
706C GLN* 2.9 52.3 + - + +
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Residues in contact with ILE 703 (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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108A VAL* 5.4 1.3 - - + -
109A MET* 4.8 20.2 - - + -
112A LEU* 3.8 34.5 - - + -
114A GLU* 4.8 11.4 - - - +
116A LEU* 4.8 5.4 - - + -
699C ARG* 2.8 26.6 + - + +
700C GLY* 3.6 18.8 - - - +
702C GLU* 1.3 77.7 - - - +
704C LEU* 1.3 65.8 + - + +
706C GLN* 3.9 18.2 - - - +
707C ASN* 2.8 29.4 + - - +
713C ASN* 4.4 12.1 - - + +
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Residues in contact with LEU 704 (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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88A ALA* 3.7 25.6 - - + +
91A VAL* 5.7 2.7 - - + -
92A PHE* 3.6 28.3 - - + -
105A LEU* 3.5 30.5 - - + -
108A VAL* 3.9 22.6 - - + +
141A PHE* 3.9 20.6 - - + -
700C GLY 4.2 6.7 - - - +
701C TRP* 3.5 12.3 + - + +
703C ILE* 1.3 82.0 - - + +
705C ARG* 1.3 64.2 + - + +
707C ASN* 3.1 21.3 + - - +
708C THR* 3.4 17.1 + - + +
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Residues in contact with ARG 705 (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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85A ILE* 5.3 7.6 - - - -
88A ALA* 4.4 7.9 - - + -
141A PHE* 3.3 49.0 + - + -
144A MET* 3.3 54.7 + - - +
145A MET* 3.3 46.4 - - + +
698C HIS 5.4 0.2 + - - -
701C TRP* 3.3 31.4 + - - +
702C GLU* 3.3 8.8 + - - +
704C LEU* 1.3 77.2 - - + +
706C GLN* 1.3 64.6 + - - +
708C THR* 3.4 7.6 - - + +
709C LEU* 3.1 25.7 + - - +
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Residues in contact with GLN 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A MET* 5.1 9.4 - - + -
699C ARG* 6.1 0.8 - - - +
702C GLU* 2.9 52.1 + - + +
703C ILE* 3.9 18.3 - - - +
705C ARG* 1.3 78.8 - - - +
707C ASN* 1.3 58.1 + - - +
709C LEU* 3.4 2.5 + - - +
710C GLY 3.0 5.9 + - - -
711C HIS* 2.9 55.4 + - + +
713C ASN* 3.5 37.0 + - - +
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Residues in contact with ASN 707 (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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91A VAL* 5.5 4.9 - - - +
108A VAL* 3.2 27.7 - - - +
111A ASN* 5.7 3.9 + - - -
112A LEU* 3.9 28.3 - - + +
703C ILE 2.8 28.2 + - - +
704C LEU 3.1 9.8 + - - +
706C GLN* 1.3 78.6 - - - +
708C THR* 1.3 69.1 + - - +
710C GLY* 3.3 12.7 + - - -
711C HIS 5.0 2.0 - - - +
713C ASN* 5.0 3.8 - - - +
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Residues in contact with THR 708 (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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84A GLU 6.0 0.2 - - - +
87A GLU* 4.7 4.3 + - - +
88A ALA* 3.5 33.8 + - + -
91A VAL* 3.4 30.0 - - - +
704C LEU* 3.4 18.6 - - + +
705C ARG* 3.4 8.5 - - - +
707C ASN* 1.3 82.8 + - - +
709C LEU* 1.3 65.6 + - + +
710C GLY* 3.1 2.1 + - - -
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Residues in contact with LEU 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 4.7 17.9 - - + +
705C ARG 3.1 18.7 + - - +
706C GLN* 3.6 7.2 - - - +
708C THR* 1.3 79.0 - - + +
710C GLY* 1.3 60.3 + - - +
711C HIS* 3.7 26.7 - - + +
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Residues in contact with GLY 710 (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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706C GLN 3.0 3.4 + - - -
707C ASN* 3.3 11.6 + - - -
708C THR 3.1 3.6 - - - -
709C LEU* 1.3 83.0 - - - +
711C HIS* 1.3 65.9 + - - +
712C LEU* 3.5 2.4 + - - +
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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