Contacts of the strand formed by residues 150 - 155 (chain 5) in PDB entry 1O19
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 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1425 LEU* 3.8 14.1 - - - +
1495 THR* 1.3 77.8 - - - +
1515 ILE* 1.3 61.5 + - - +
1645 PRO* 3.7 0.7 - - - +
1655 ILE* 2.9 28.9 + - - +
2925 ASP 4.8 0.2 - - - -
2935 LEU* 3.8 12.7 - - - +
2965 ASN* 3.2 20.9 - - - -
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Residues in contact with ILE 151 (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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1425 LEU* 4.4 0.2 - - - +
1505 GLY* 1.3 74.9 - - - +
1525 VAL* 1.3 67.1 + - - +
1535 LEU 4.0 0.3 + - - -
1625 ASN* 4.5 6.1 - - + +
1635 VAL 3.7 7.6 - - - +
1645 PRO* 3.9 22.9 - - + -
2785 THR* 3.6 29.6 - - + +
2815 SER* 3.6 21.5 - - - +
2825 ILE* 3.7 12.8 - - + -
2935 LEU* 3.4 33.0 - - + +
2965 ASN 2.8 8.4 + - - +
2975 ASN* 3.4 21.4 - - - +
2985 VAL* 2.9 23.6 + - - +
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Residues in contact with VAL 152 (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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1385 ALA* 3.3 42.2 - - + +
1415 SER* 4.3 2.5 - - - -
1425 LEU* 3.8 29.2 - - + +
1515 ILE* 1.3 74.4 - - - +
1535 LEU* 1.3 67.0 + - - +
1545 ASP* 3.6 9.9 + - + -
1615 HIS 3.6 0.3 - - - +
1625 ASN* 3.2 6.8 - - - +
1635 VAL* 2.9 31.8 + - - +
1655 ILE* 4.5 1.8 - - + -
2975 ASN* 5.6 0.2 - - - -
2985 VAL* 3.1 14.6 - - + +
3005 SER* 3.6 24.2 - - - +
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Residues in contact with LEU 153 (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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1515 ILE 4.0 1.2 + - - -
1525 VAL* 1.3 71.9 - - - +
1545 ASP* 1.3 59.4 + - - +
1555 SER* 5.1 2.0 - - - -
1605 THR* 4.4 8.5 - - + -
1615 HIS 3.4 8.7 - - - +
1625 ASN* 3.6 24.2 - - - +
2745 ILE* 3.6 41.3 - - + +
2785 THR* 3.9 10.1 - - - +
2975 ASN* 4.5 13.9 - - - +
2985 VAL 2.9 7.8 + - - +
2995 MET* 3.6 35.0 - - + +
3005 SER 3.1 24.6 + - - +
3045 THR* 4.0 14.1 - - + -
3095 ILE* 5.7 4.9 - - + -
3135 MET* 4.5 3.1 - - + -
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Residues in contact with ASP 154 (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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1095 PRO* 5.9 2.3 - - - +
1375 GLN* 4.0 25.8 - - - +
1385 ALA* 4.1 10.6 + - + +
1525 VAL* 3.6 12.2 + - + +
1535 LEU* 1.3 73.6 - - - +
1555 SER* 1.4 64.2 + - - +
1565 GLY 5.1 0.2 + - - -
1595 VAL 4.0 1.4 - - - +
1605 THR* 3.2 3.7 - - - +
1615 HIS* 2.7 51.7 + - + +
3005 SER* 3.0 30.0 + - - +
3015 GLY* 4.0 4.5 + - - -
3395 VAL* 4.2 9.6 - - - +
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Residues in contact with SER 155 (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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1535 LEU* 5.1 4.0 - - - -
1545 ASP* 1.4 76.8 + - - +
1565 GLY* 1.3 62.1 + - - +
1595 VAL 3.6 3.8 - - - -
1605 THR* 2.6 27.6 + - - +
1805 LEU 4.6 0.3 + - - -
1815 ALA* 4.5 1.9 - - - +
2615 LEU* 4.8 4.4 - - - +
2745 ILE* 5.5 0.8 - - - +
3005 SER 3.1 8.3 + - - -
3015 GLY* 3.2 13.4 - - - -
3035 THR* 3.1 39.3 + - - +
3045 THR* 3.6 19.5 - - - -
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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