Contacts of the strand formed by residues 150 - 155 (chain 1) 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 GLY 150 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1421 LEU* 3.8 14.3 - - - +
1491 THR* 1.3 77.3 - - - +
1511 ILE* 1.3 61.6 + - - +
1641 PRO* 3.8 0.7 - - - +
1651 ILE* 2.9 28.9 + - - +
2921 ASP 4.8 0.2 - - - -
2931 LEU* 3.8 13.2 - - - +
2961 ASN* 3.2 20.9 - - - -
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Residues in contact with ILE 151 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1421 LEU* 4.4 0.4 - - - +
1501 GLY* 1.3 75.1 - - - +
1521 VAL* 1.3 65.5 + - - +
1531 LEU 4.0 0.3 + - - -
1621 ASN* 4.5 7.2 - - + +
1631 VAL 3.7 8.7 - - - +
1641 PRO* 3.9 22.2 - - + -
2781 THR* 3.6 29.4 - - + +
2811 SER* 3.6 20.9 - - - +
2821 ILE* 3.7 13.2 - - + -
2931 LEU* 3.4 33.0 - - + +
2961 ASN 2.8 8.1 + - - +
2971 ASN* 3.4 20.5 - - - +
2981 VAL* 2.9 23.4 + - - +
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Residues in contact with VAL 152 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1381 ALA* 3.3 42.0 - - + +
1411 SER* 4.3 2.5 - - - -
1421 LEU* 3.8 29.8 - - + +
1511 ILE* 1.3 75.1 - - - +
1531 LEU* 1.3 67.8 + - - +
1541 ASP* 3.6 10.1 + - + -
1611 HIS 3.6 0.3 - - - +
1621 ASN* 3.2 6.3 - - - +
1631 VAL* 2.9 33.3 + - - +
1651 ILE* 4.5 1.6 - - + -
2971 ASN* 5.6 0.2 - - - -
2981 VAL* 3.1 15.7 - - + +
3001 SER* 3.6 24.5 - - - +
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Residues in contact with LEU 153 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1511 ILE 4.0 1.2 + - - -
1521 VAL* 1.3 71.7 - - - +
1541 ASP* 1.3 59.6 + - - +
1551 SER* 5.1 2.2 - - - -
1601 THR* 4.4 9.0 - - + -
1611 HIS 3.4 8.7 - - - +
1621 ASN* 3.6 24.0 - - - +
2741 ILE* 3.6 42.0 - - + +
2771 THR* 5.9 0.2 - - + -
2781 THR* 3.9 10.5 - - - +
2971 ASN* 4.5 13.8 - - - +
2981 VAL 2.9 7.6 + - - +
2991 MET* 3.6 35.0 - - + +
3001 SER 3.1 24.1 + - - +
3041 THR* 4.0 13.9 - - + -
3091 ILE* 5.7 4.9 - - + -
3131 MET* 4.5 3.4 - - + -
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Residues in contact with ASP 154 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091 PRO* 5.9 2.4 - - + +
1371 GLN* 4.0 25.6 - - - +
1381 ALA* 4.1 10.8 + - + +
1521 VAL* 3.6 12.5 + - + +
1531 LEU* 1.3 74.9 - - - +
1551 SER* 1.4 63.5 + - - +
1561 GLY 4.4 0.2 - - - -
1591 VAL 4.0 1.1 - - - +
1601 THR* 3.2 3.9 - - - +
1611 HIS* 2.7 51.6 + - + +
3001 SER* 3.0 30.6 + - - +
3011 GLY* 4.0 4.9 + - - -
3391 VAL* 4.3 9.3 - - - +
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Residues in contact with SER 155 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1531 LEU* 5.1 3.8 - - - -
1541 ASP* 1.4 75.9 + - - +
1561 GLY* 1.3 61.6 + - - +
1591 VAL 3.6 3.8 - - - -
1601 THR* 2.6 28.0 + - - +
1801 LEU 4.6 0.5 + - - -
1811 ALA* 4.5 2.3 - - - +
2611 LEU* 4.8 4.7 - - - +
2741 ILE* 5.5 0.8 - - - +
3001 SER 3.1 8.7 + - - -
3011 GLY* 3.2 13.6 - - - -
3031 THR* 3.1 39.1 + - - +
3041 THR* 3.6 19.3 - - - -
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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