Contacts of the strand formed by residues 668 - 675 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M LEU* 6.2 0.6 - - - +
165M PHE* 4.5 22.1 - + - -
169M ASP* 4.7 5.5 + - - -
171M GLU* 4.2 16.5 + - - +
172M ASN 2.7 13.9 + - - +
173M GLN* 2.6 28.7 + - - +
174M SER 3.2 16.5 + - - -
494M HIS* 3.6 20.4 + + - -
498M LEU* 5.3 3.8 - - - +
667M THR* 1.3 70.1 - - - +
669M PRO* 1.3 84.7 + - + +
670M HIS* 3.3 24.9 + + - -
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Residues in contact with PRO 669 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M LEU* 5.5 2.6 - - - +
174M SER* 3.1 11.0 - - - +
176M LEU* 4.5 1.3 - - + -
490M PHE* 3.5 38.4 - - + -
494M HIS* 3.6 36.8 + - + +
667M THR 3.1 13.2 - - - +
668M HIS* 1.3 106.4 + - + +
670M HIS* 1.3 63.5 + - - +
671M PHE* 3.7 19.4 - - + -
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Residues in contact with HIS 670 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M LEU* 6.2 2.4 - - - +
158M ILE* 4.5 17.2 + - + +
161M ASN* 5.2 3.1 - - + -
162M ALA* 4.1 13.8 - - + -
165M PHE* 3.9 23.6 - + - -
173M GLN* 3.2 33.5 + - + +
174M SER* 2.7 18.3 + - - +
175M ILE* 2.9 17.6 - - + -
176M LEU* 2.7 33.3 + - - +
668M HIS* 3.3 42.1 + + - -
669M PRO* 1.3 72.4 + - - +
671M PHE* 1.3 56.6 + - - +
672M VAL* 5.1 0.7 - - - -
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Residues in contact with PHE 671 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M LEU* 3.7 20.0 + - + +
122M PHE* 3.7 22.9 - + + +
123M CYS* 3.5 18.4 + - - +
158M ILE* 4.4 4.3 - - - +
176M LEU* 3.9 24.7 - - + -
487M LEU 4.8 2.9 - - - -
490M PHE* 4.1 8.1 - + - -
491M PHE* 3.2 56.8 - + + -
494M HIS* 4.2 15.7 - + - -
669M PRO* 3.7 29.2 - - + -
670M HIS* 1.3 72.9 - - - +
672M VAL* 1.3 68.8 + - - +
673M ARG* 3.9 26.0 - - - +
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Residues in contact with VAL 672 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123M CYS* 3.8 16.8 - - + +
125M THR* 4.9 2.0 - - - +
155M ILE* 4.5 24.5 - - + -
158M ILE* 4.2 20.6 - - + -
175M ILE* 3.8 23.1 - - + -
176M LEU 2.8 20.5 + - - +
177M ILE* 3.3 21.0 - - + -
178M THR 3.3 13.0 + - - -
192M VAL* 6.4 1.1 - - + -
671M PHE* 1.3 79.5 - - - +
673M ARG* 1.3 69.7 + - - +
674M CYS* 4.5 12.6 - - - -
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Residues in contact with ARG 673 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122M PHE* 3.9 28.2 - - + -
123M CYS 3.3 11.2 + - - +
124M VAL* 3.4 5.3 - - - -
125M THR 3.0 23.6 + - - -
176M LEU* 3.0 36.0 + - - +
178M THR* 3.6 30.4 + - - +
484M ASN* 5.4 2.6 + - - -
487M LEU* 5.2 15.0 - - - +
488M GLN* 4.6 9.1 + - - +
491M PHE* 5.9 1.6 - - - +
671M PHE* 3.9 22.5 - - - -
672M VAL* 1.3 75.8 + - - +
674M CYS* 1.3 62.2 + - - +
675M ILE* 3.9 6.4 - - + +
698M ASN* 3.2 51.5 + - + +
700M VAL* 4.7 6.3 - - + -
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Residues in contact with CYS 674 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M THR* 3.6 8.3 - - + +
177M ILE* 3.5 27.6 - - - -
178M THR 2.9 13.8 + - - +
179M GLY* 3.7 10.9 - - - -
183M ALA* 3.4 30.9 - - + +
185M LYS* 4.2 7.2 - - + -
188M ASN* 2.9 33.0 - - - +
672M VAL* 4.5 7.2 - - - -
673M ARG* 1.3 74.7 - - - +
675M ILE* 1.3 64.6 + - - +
694M GLN* 4.6 2.6 - - - +
698M ASN* 4.8 3.5 + - - -
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Residues in contact with ILE 675 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106M LEU* 5.4 2.2 - - + -
124M VAL* 3.0 33.4 - - + -
125M THR 2.5 18.6 + - - +
126M VAL* 3.6 22.2 - - + -
127M ASN* 3.1 29.8 + - - +
183M ALA* 3.9 7.9 + - - +
673M ARG* 3.9 9.2 - - + +
674M CYS* 1.3 75.3 - - - +
676M ILE* 1.3 70.9 + - - +
677M PRO* 4.2 0.9 - - + -
686M MET* 5.9 0.2 - - - -
691M VAL* 4.3 17.7 - - + -
694M GLN* 4.1 17.0 - - + +
695M LEU* 4.7 11.7 - - + -
698M ASN* 3.7 23.8 - - - +
700M VAL* 5.7 0.9 - - + -
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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