Contacts of the strand formed by residues 8 - 12 (chain 5) 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 LEU 8 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75 ALA* 1.3 75.7 - - - +
95 VAL* 1.3 68.3 + - - +
105 CYS* 4.1 1.8 - - + +
205 GLY 3.6 3.8 - - - +
215 PHE* 3.5 36.6 - - + -
905 PHE* 4.0 25.6 - - + -
945 LEU* 4.2 13.2 - - + -
965 VAL* 4.0 20.2 - - + -
985 PRO* 5.3 2.2 - - + -
1015 HIS* 3.7 35.7 - - + +
1025 PRO 2.8 11.0 + - - +
1035 THR* 4.2 14.1 - - + +
1045 LEU* 2.9 23.6 + - - +
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Residues in contact with VAL 9 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85 LEU* 1.3 78.9 - - - +
105 CYS* 1.3 65.4 + - - +
115 ASP* 5.4 0.2 - - + -
195 ALA* 3.2 11.7 - - - -
205 GLY 3.0 10.6 + - - -
225 ALA* 4.2 16.6 - - + +
945 LEU* 6.4 0.2 - - - -
1045 LEU* 3.3 27.1 - - + +
1065 THR* 5.4 3.4 - - + -
3395 VAL 5.7 0.2 - - - +
3405 TRP* 2.8 60.0 + - + +
3435 GLY* 3.9 25.8 - - - +
3445 SER* 3.9 9.0 - - - +
3475 ALA* 4.5 0.9 - - + -
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Residues in contact with CYS 10 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85 LEU* 4.1 2.2 - - + -
95 VAL* 1.3 76.1 - - - +
115 ASP* 1.3 59.9 + - - +
125 ASN* 3.5 23.9 + - - -
175 VAL* 4.1 17.0 - - - -
185 LYS 3.6 3.1 - - - -
195 ALA* 4.5 3.8 - - + +
865 TRP* 4.0 18.8 - - - -
895 THR* 4.7 11.2 - - + -
905 PHE* 5.8 5.2 - - + -
1035 THR* 4.9 6.3 - - + -
1045 LEU 2.9 7.5 + - - +
1055 LEU* 3.5 20.9 - - + +
1065 THR* 3.4 21.3 + - - +
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Residues in contact with ASP 11 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95 VAL* 4.0 1.2 - - + -
105 CYS* 1.3 72.3 - - - +
125 ASN* 1.3 65.6 + - - +
135 GLY* 5.3 0.3 - - - -
175 VAL* 3.5 6.1 - - - -
185 LYS* 2.8 59.7 + - + +
1065 THR* 2.9 27.0 + - + +
1375 GLN* 4.2 7.8 - - - +
3395 VAL* 3.4 33.0 - - + +
3405 TRP* 4.0 17.2 + - + +
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Residues in contact with ASN 12 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105 CYS* 3.5 19.9 + - - -
115 ASP* 1.3 77.5 + - - +
135 GLY* 1.3 59.4 + - - +
175 VAL* 4.6 9.1 - - + +
335 SER* 5.7 0.2 - - - -
715 ILE* 3.5 22.9 - - + +
745 GLY* 5.3 3.1 - - - +
765 ILE* 5.5 3.2 - - + +
825 MET* 3.5 12.6 - - + +
855 ILE* 5.6 0.2 - - - +
865 TRP* 2.9 38.7 + - - +
1055 LEU* 4.3 7.7 - - - +
1065 THR* 3.7 21.1 + - - +
1195 MET* 4.8 4.0 - - - +
1375 GLN* 4.1 15.1 + - - -
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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