Contacts of the strand formed by residues 668 - 675 (chain P) in PDB entry 1O18
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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121P LEU* 6.2 0.4 - - - +
165P PHE* 4.5 22.1 - + - -
169P ASP* 4.7 5.1 + - - -
171P GLU* 4.2 17.0 + - - +
172P ASN 2.7 14.3 + - - +
173P GLN* 2.6 28.1 + - - +
174P SER 3.2 16.1 + - - -
494P HIS* 3.6 20.1 + + - -
498P LEU* 5.3 3.8 - - - +
667P THR* 1.3 70.6 - - - +
669P PRO* 1.3 85.8 + - + +
670P HIS* 3.3 25.3 + + - -
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Residues in contact with PRO 669 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121P LEU* 5.5 2.3 - - - +
174P SER* 3.1 10.8 - - - +
176P LEU* 4.5 1.8 - - + -
490P PHE* 3.5 38.1 - - + -
494P HIS* 3.6 37.1 + - + +
667P THR 3.1 13.4 - - - +
668P HIS* 1.3 105.7 + - + +
670P HIS* 1.3 62.7 + - - +
671P PHE* 3.7 18.4 - - + -
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Residues in contact with HIS 670 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121P LEU* 6.2 2.2 - - - +
158P ILE* 4.5 17.2 + - + +
161P ASN* 5.2 3.8 - - + -
162P ALA* 4.1 12.7 - - + -
165P PHE* 3.9 23.6 - + - -
173P GLN* 3.2 33.9 + - + +
174P SER* 2.7 17.3 + - - +
175P ILE* 2.9 18.2 - - + -
176P LEU* 2.7 33.0 + - - +
668P HIS* 3.3 41.6 + + - -
669P PRO* 1.3 71.2 + - - +
671P PHE* 1.3 56.5 + - - +
672P VAL* 5.1 0.4 - - - -
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Residues in contact with PHE 671 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121P LEU* 3.7 19.9 + - + +
122P PHE* 3.7 22.7 - + + +
123P CYS* 3.5 18.2 + - - +
158P ILE* 4.4 4.1 - - - +
176P LEU* 3.9 24.9 - - + -
487P LEU 4.8 2.9 - - - -
490P PHE* 4.1 8.3 - + - -
491P PHE* 3.2 59.5 - + + -
494P HIS* 4.2 15.3 - + - -
669P PRO* 3.7 29.4 - - + -
670P HIS* 1.3 72.0 - - - +
672P VAL* 1.3 68.0 + - - +
673P ARG* 3.9 25.1 - - - +
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Residues in contact with VAL 672 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P CYS* 3.8 15.9 - - + +
125P THR* 4.9 2.0 - - - +
155P ILE* 4.5 24.2 - - + -
158P ILE* 4.2 21.1 - - + -
175P ILE* 3.8 23.3 - - + -
176P LEU 2.8 20.8 + - - +
177P ILE* 3.3 21.7 - - + -
178P THR 3.3 13.0 + - - -
192P VAL* 6.4 1.1 - - + -
671P PHE* 1.3 78.2 - - - +
673P ARG* 1.3 68.8 + - - +
674P CYS* 4.1 13.2 + - - -
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Residues in contact with ARG 673 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122P PHE* 3.9 29.2 - - + -
123P CYS 3.3 10.9 + - - +
124P VAL* 3.4 5.4 - - - -
125P THR 3.0 23.7 + - - -
176P LEU* 3.0 36.4 + - - +
178P THR* 3.6 30.0 + - - +
484P ASN* 5.5 3.0 + - - -
487P LEU* 5.2 14.8 - - - +
488P GLN* 4.6 9.5 + - - +
491P PHE* 5.9 1.4 - - - +
671P PHE* 3.9 22.5 - - - -
672P VAL* 1.3 78.0 + - - +
674P CYS* 1.3 62.5 + - - +
675P ILE* 3.9 5.8 - - + +
698P ASN* 3.2 50.0 + - + +
700P VAL* 4.7 7.0 - - + -
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Residues in contact with CYS 674 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125P THR* 3.6 8.3 - - - +
177P ILE* 3.5 27.6 - - - -
178P THR 2.9 13.2 + - - +
179P GLY* 3.7 11.1 - - - -
183P ALA* 3.4 31.1 - - + +
185P LYS* 4.2 6.7 - - + -
188P ASN* 2.9 33.0 - - - +
672P VAL* 4.5 7.6 - - - -
673P ARG* 1.3 73.8 - - - +
675P ILE* 1.3 64.2 + - - +
694P GLN* 4.6 2.6 - - - +
698P ASN* 4.8 3.5 + - - -
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Residues in contact with ILE 675 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P LEU* 5.4 2.7 - - + -
124P VAL* 3.0 33.7 - - + -
125P THR 2.5 17.7 + - - +
126P VAL* 3.6 22.2 - - + -
127P ASN* 3.1 29.5 + - - +
183P ALA* 3.9 7.4 + - - +
673P ARG* 3.9 9.4 - - + +
674P CYS* 1.3 76.3 - - - +
676P ILE* 1.3 71.7 + - - +
677P PRO* 3.5 1.0 - - + +
691P VAL* 4.3 17.3 - - + -
694P GLN* 4.1 17.3 - - + +
695P LEU* 4.7 11.9 - - + -
698P ASN* 3.7 23.6 - - - +
700P VAL* 5.7 0.2 - - + -
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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