Contacts of the strand formed by residues 668 - 675 (chain G) in PDB entry 1O19
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 668 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121G LEU* 6.2 0.2 - - - +
165G PHE* 4.5 22.1 - + - -
169G ASP* 4.7 5.1 + - - -
171G GLU* 4.2 17.1 + - - +
172G ASN 2.7 14.8 + - - +
173G GLN* 2.6 28.8 + - - +
174G SER 3.2 16.3 + - - -
494G HIS* 3.6 20.4 + + - -
498G LEU* 5.3 4.0 - - - +
667G THR* 1.3 69.7 - - - +
669G PRO* 1.3 86.0 + - + +
670G HIS* 3.3 24.8 + + - -
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Residues in contact with PRO 669 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G LEU* 5.5 2.8 - - - +
174G SER* 3.1 11.4 - - - +
176G LEU* 4.5 1.6 - - + -
490G PHE* 3.5 37.9 - - + -
494G HIS* 3.6 38.1 + - + +
667G THR 3.1 13.7 - - - +
668G HIS* 1.3 105.8 + - + +
670G HIS* 1.3 62.7 + - - +
671G PHE* 3.7 18.8 - - + -
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Residues in contact with HIS 670 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G LEU* 6.2 2.2 - - - +
158G ILE* 4.5 18.2 + - + +
161G ASN* 5.2 3.6 - - + +
162G ALA* 4.1 13.6 - - + -
165G PHE* 3.9 23.8 - + - -
173G GLN* 3.2 33.9 + - + +
174G SER* 2.7 17.1 + - - +
175G ILE* 2.9 19.5 - - + -
176G LEU* 2.7 33.0 + - - +
668G HIS* 3.3 41.9 + + - -
669G PRO* 1.3 72.4 + - - +
671G PHE* 1.3 54.4 + - - +
672G VAL* 5.1 0.4 - - - -
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Residues in contact with PHE 671 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G LEU* 3.7 20.7 + - + +
122G PHE* 3.7 22.0 - + + -
123G CYS* 3.5 17.7 + - - +
158G ILE* 4.4 5.2 - - - +
176G LEU* 3.9 25.1 - - + -
487G LEU* 4.8 2.7 - - + -
490G PHE* 4.1 9.0 - + - -
491G PHE* 3.2 57.7 - + + -
494G HIS* 4.2 15.3 - + - -
669G PRO* 3.7 30.3 - - + -
670G HIS* 1.3 72.3 - - - +
672G VAL* 1.3 68.1 + - - +
673G ARG* 3.9 25.1 - - - +
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Residues in contact with VAL 672 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G CYS* 3.8 16.6 - - + +
125G THR* 4.9 2.2 - - - +
155G ILE* 4.5 24.2 - - + -
158G ILE* 4.2 20.2 - - + -
175G ILE* 3.8 22.7 - - + -
176G LEU 2.8 20.9 + - - +
177G ILE* 3.4 21.0 - - + +
178G THR 3.3 12.8 + - - -
192G VAL* 6.4 1.1 - - + -
671G PHE* 1.3 79.1 - - - +
673G ARG* 1.3 68.5 + - - +
674G CYS* 4.5 12.8 - - - -
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Residues in contact with ARG 673 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G PHE* 3.9 28.8 - - + -
123G CYS 3.3 11.1 + - - +
124G VAL* 3.4 5.6 - - - -
125G THR 3.0 23.7 + - - -
176G LEU* 3.0 37.4 + - - +
178G THR* 3.6 29.0 + - - +
484G ASN* 5.4 2.6 + - - -
487G LEU* 5.2 15.6 - - - +
488G GLN* 4.6 8.5 + - - +
491G PHE* 5.9 1.6 - - - +
671G PHE* 3.9 21.5 - - - -
672G VAL* 1.3 77.1 + - - +
674G CYS* 1.3 62.4 + - - +
675G ILE* 3.9 5.9 + - + +
698G ASN* 3.2 49.3 + - + +
700G VAL* 4.7 7.2 - - + -
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Residues in contact with CYS 674 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G THR* 3.6 7.9 - - + +
177G ILE* 3.5 27.4 - - - -
178G THR 2.9 13.5 + - - +
179G GLY* 3.7 10.7 - - - -
183G ALA* 3.4 31.3 - - + +
185G LYS* 4.2 7.6 - - + -
188G ASN* 2.9 32.3 - - - +
672G VAL* 4.5 7.9 - - - -
673G ARG* 1.3 73.6 - - - +
675G ILE* 1.3 62.5 + - - +
694G GLN* 4.6 2.6 - - - +
698G ASN* 4.8 3.8 + - - -
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Residues in contact with ILE 675 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G LEU* 5.4 2.0 - - + -
124G VAL* 3.0 34.5 - - + -
125G THR 2.5 18.8 + - - +
126G VAL* 3.6 22.7 - - + -
127G ASN* 3.1 29.3 + - - +
183G ALA* 3.9 7.0 - - - +
673G ARG* 3.9 9.6 - - + +
674G CYS* 1.3 76.4 - - - +
676G ILE* 1.3 71.2 + - - +
677G PRO* 4.2 0.7 - - + -
691G VAL* 4.3 17.7 - - + -
694G GLN* 4.1 17.0 - - + +
695G LEU* 4.7 11.4 - - + -
698G ASN* 3.7 23.1 - - - +
700G VAL* 5.7 0.4 - - + -
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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