Contacts of the strand formed by residues 150 - 155 (chain 7) 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 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1427 LEU* 3.8 13.9 - - - +
1497 THR* 1.3 77.8 - - - +
1517 ILE* 1.3 61.5 + - - +
1527 VAL 4.3 0.2 - - - -
1647 PRO* 3.7 0.5 - - - +
1657 ILE* 2.9 27.6 + - - +
2937 LEU* 3.8 12.7 - - - +
2967 ASN* 3.2 21.1 - - - -
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Residues in contact with ILE 151 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1427 LEU* 4.4 0.6 - - - +
1507 GLY* 1.3 74.6 - - - +
1527 VAL* 1.3 65.3 + - - +
1537 LEU 4.0 0.3 + - - -
1627 ASN* 4.5 5.8 - - + +
1637 VAL 3.7 8.3 - - - +
1647 PRO* 3.9 22.0 - - + -
2787 THR* 3.6 29.4 - - + +
2817 SER* 3.6 22.0 - - - +
2827 ILE* 3.7 12.6 - - + -
2937 LEU* 3.4 34.3 - - + +
2967 ASN 2.8 8.7 + - - +
2977 ASN* 3.4 20.6 - - - +
2987 VAL 2.9 23.6 + - - +
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Residues in contact with VAL 152 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1387 ALA* 3.3 41.5 - - + +
1417 SER* 4.3 2.7 - - - -
1427 LEU* 3.8 29.6 - - + +
1517 ILE* 1.3 74.5 - - - +
1537 LEU* 1.3 68.4 + - - +
1547 ASP* 3.6 10.4 + - + +
1617 HIS 4.1 0.2 - - - -
1627 ASN* 3.2 6.9 - - - +
1637 VAL* 2.9 32.8 + - - +
1657 ILE* 4.5 1.8 - - + -
2987 VAL* 3.1 14.6 - - + +
3007 SER* 3.6 24.5 - - - +
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Residues in contact with LEU 153 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1517 ILE 4.0 1.2 + - - -
1527 VAL* 1.3 71.8 - - - +
1547 ASP* 1.3 59.2 + - - +
1557 SER* 5.1 2.5 - - - -
1607 THR* 4.4 9.0 - - + -
1617 HIS 3.4 8.1 - - - +
1627 ASN* 3.6 24.7 - - - +
2747 ILE* 3.6 41.3 - - + +
2787 THR* 3.9 9.9 - - - +
2977 ASN* 4.5 13.8 - - - +
2987 VAL 2.9 7.8 + - - +
2997 MET* 3.6 34.1 - - + -
3007 SER 3.1 24.9 + - - +
3047 THR* 4.0 13.2 - - + -
3097 ILE* 5.7 5.4 - - + -
3137 MET* 4.5 3.6 - - + -
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Residues in contact with ASP 154 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097 PRO* 5.9 2.1 - - - +
1377 GLN* 4.0 26.0 - - - +
1387 ALA* 4.1 10.3 + - + +
1527 VAL* 3.6 13.4 + - + +
1537 LEU* 1.3 73.8 - - - +
1557 SER* 1.4 64.2 + - - +
1597 VAL 4.0 1.1 - - - +
1607 THR* 3.2 3.3 - - - +
1617 HIS* 2.7 51.2 + - + +
3007 SER* 3.0 30.3 + - - +
3017 GLY* 4.0 4.7 + - - -
3397 VAL* 4.2 9.5 - - - +
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Residues in contact with SER 155 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1537 LEU* 5.1 3.6 - - - -
1547 ASP* 1.4 75.6 + - - +
1567 GLY* 1.3 60.4 + - - +
1597 VAL 3.6 3.6 - - - -
1607 THR* 2.6 27.6 + - - +
1807 LEU 4.6 0.7 + - - -
1817 ALA* 4.5 2.3 - - - +
2617 LEU* 4.8 4.6 - - - +
2747 ILE* 6.1 0.7 - - - -
3007 SER 3.1 8.3 + - - -
3017 GLY* 3.2 13.6 - - - -
3037 THR* 3.1 39.6 + - - +
3047 THR* 3.6 19.1 - - - -
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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