Contacts of the strand formed by residues 668 - 675 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A LEU* 6.2 0.2 - - - +
165A PHE* 4.5 21.7 - + - -
169A ASP* 4.7 5.5 + - - -
171A GLU* 4.2 16.3 + - - +
172A ASN 2.7 15.2 + - - +
173A GLN* 2.6 27.5 + - - +
174A SER 3.2 16.1 + - - -
494A HIS* 3.6 21.0 + + - -
498A LEU* 5.3 3.4 - - - +
667A THR* 1.3 71.2 - - - +
669A PRO* 1.3 85.7 + - + +
670A HIS* 3.3 24.7 + + - -
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Residues in contact with PRO 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU* 5.5 2.8 - - - +
174A SER* 3.1 11.7 - - - +
176A LEU* 4.5 1.1 - - + -
490A PHE* 3.5 37.7 - - + -
494A HIS* 3.6 36.8 + - + +
667A THR 3.1 13.0 - - - +
668A HIS* 1.3 106.4 + - + +
670A HIS* 1.3 61.8 + - - +
671A PHE* 3.7 18.8 - - + -
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Residues in contact with HIS 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 6.2 2.2 - - - +
158A ILE* 4.5 17.6 + - + +
161A ASN* 5.2 3.6 - - + -
162A ALA* 4.1 14.6 - - + -
165A PHE* 3.9 22.6 - + - -
173A GLN* 3.2 33.7 + - + +
174A SER* 2.7 17.3 + - - +
175A ILE* 2.9 19.5 - - + -
176A LEU* 2.7 32.9 + - - +
668A HIS* 3.3 41.6 + + - -
669A PRO* 1.3 72.8 + - - +
671A PHE* 1.3 56.4 + - - +
672A VAL* 5.1 0.2 - - - -
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Residues in contact with PHE 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU* 3.7 20.2 + - + +
122A PHE* 3.7 22.7 - + + -
123A CYS* 3.5 17.7 + - - +
158A ILE* 4.4 4.1 - - - +
176A LEU* 3.9 25.4 - - + -
487A LEU* 4.8 2.7 - - + -
490A PHE* 4.1 8.5 - + - -
491A PHE* 3.2 57.0 - + + -
494A HIS* 4.2 15.5 - + - -
669A PRO* 3.7 29.8 - - + -
670A HIS* 1.3 71.8 - - - +
672A VAL* 1.3 68.1 + - - +
673A ARG* 3.9 24.0 - - - +
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Residues in contact with VAL 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A CYS* 3.8 17.0 - - + +
125A THR* 4.9 2.0 - - - +
155A ILE* 4.5 23.6 - - + -
158A ILE* 4.2 20.9 - - + -
175A ILE* 3.8 22.2 - - + -
176A LEU 2.8 21.4 + - - +
177A ILE* 3.3 21.0 - - + -
178A THR 3.3 12.8 + - - -
192A VAL* 6.4 1.3 - - + -
671A PHE* 1.3 77.7 - - - +
673A ARG* 1.3 67.8 + - - +
674A CYS* 4.5 12.6 - - - -
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Residues in contact with ARG 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PHE* 3.9 29.0 - - + -
123A CYS 3.3 11.2 + - - +
124A VAL* 3.4 5.6 - - - -
125A THR 3.0 23.9 + - - -
176A LEU* 3.0 35.8 + - - +
178A THR* 3.6 30.9 + - - +
484A ASN* 5.4 2.8 + - - -
487A LEU* 5.2 16.0 - - - +
488A GLN* 4.6 8.5 + - - -
491A PHE* 5.9 1.2 - - - +
671A PHE* 3.9 22.2 - - - -
672A VAL* 1.3 76.2 + - - +
674A CYS* 1.3 62.7 + - - +
675A ILE* 3.9 5.8 + - + +
698A ASN* 3.2 51.2 + - + +
700A VAL* 4.7 6.7 - - + -
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Residues in contact with CYS 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A THR* 3.6 7.6 - - + +
177A ILE* 3.5 27.8 - - - -
178A THR 2.9 13.5 + - - +
179A GLY* 3.7 11.3 - - - -
183A ALA* 3.4 31.8 - - + +
185A LYS* 4.2 7.4 - - + -
188A ASN* 2.9 32.8 - - - +
672A VAL* 4.5 7.4 - - - -
673A ARG* 1.3 72.8 - - - +
675A ILE* 1.3 64.3 + - - +
694A GLN* 4.6 2.6 - - - +
698A ASN* 4.8 3.8 + - - -
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Residues in contact with ILE 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 5.4 2.0 - - + -
124A VAL* 3.0 34.1 - - + -
125A THR 2.5 18.2 + - - +
126A VAL* 3.6 22.9 - - + -
127A ASN* 3.1 28.9 + - - +
183A ALA* 3.9 6.8 - - - +
673A ARG* 3.9 10.3 - - + +
674A CYS* 1.3 77.2 - - - +
676A ILE* 1.3 71.0 + - - +
677A PRO* 4.8 0.7 - - + -
691A VAL* 4.3 17.3 - - + -
694A GLN* 4.1 17.3 - - + +
695A LEU* 4.7 11.2 - - + -
698A ASN* 3.8 23.1 - - - +
700A 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