Contacts of the strand formed by residues 150 - 155 (chain 8) in PDB entry 1O1F
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 8).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428 LEU* 3.8 14.3 - - - +
1498 THR* 1.3 78.4 - - - +
1518 ILE* 1.3 62.5 + - - +
1648 PRO* 3.7 0.7 - - - +
1658 ILE* 2.9 29.1 + - - +
2938 LEU* 3.8 12.8 - - - +
2968 ASN* 3.2 20.6 - - - -
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Residues in contact with ILE 151 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428 LEU* 4.9 0.2 - - - -
1508 GLY* 1.3 75.0 - - - +
1528 VAL* 1.3 66.0 + - - +
1538 LEU 4.0 0.5 + - - -
1628 ASN* 4.5 6.1 - - + +
1638 VAL 3.7 8.5 - - - +
1648 PRO* 3.9 22.9 - - + -
2788 THR* 3.6 30.5 - - + +
2818 SER* 3.6 21.1 - - - +
2828 ILE* 3.7 12.6 - - + -
2938 LEU* 3.4 33.0 - - + +
2968 ASN 2.8 8.8 + - - +
2978 ASN* 3.4 21.5 - - - +
2988 VAL 2.9 22.9 + - - +
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Residues in contact with VAL 152 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1388 ALA* 3.3 41.5 - - + +
1418 SER* 4.3 2.9 - - - -
1428 LEU* 3.8 31.0 - - + +
1518 ILE* 1.3 74.2 - - - +
1538 LEU* 1.3 67.9 + - - +
1548 ASP* 3.6 10.2 + - + -
1618 HIS 4.1 0.2 - - - -
1628 ASN* 3.2 6.8 - - - +
1638 VAL* 2.9 32.1 + - - +
1658 ILE* 4.5 1.3 - - + -
2988 VAL* 3.1 14.4 - - + +
3008 SER* 3.6 24.7 - - - +
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Residues in contact with LEU 153 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1518 ILE 4.0 1.2 + - - -
1528 VAL* 1.3 72.0 - - - +
1548 ASP* 1.3 59.4 + - - +
1558 SER* 5.1 1.8 - - - -
1608 THR* 4.4 8.5 - - + -
1618 HIS 3.4 8.3 - - - +
1628 ASN* 3.6 24.5 - - - +
2748 ILE* 3.6 41.3 - - + +
2788 THR* 3.9 9.4 - - - +
2978 ASN* 4.5 12.9 - - - +
2988 VAL 2.9 7.8 + - - +
2998 MET* 3.6 33.9 - - + -
3008 SER 3.1 24.3 + - - +
3048 THR* 4.0 13.7 - - + -
3098 ILE* 5.7 5.4 - - + -
3138 MET* 4.5 3.8 - - + -
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Residues in contact with ASP 154 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098 PRO* 5.9 2.3 - - - +
1378 GLN* 4.0 26.2 - - - +
1388 ALA* 4.1 11.0 + - + -
1528 VAL* 3.6 13.6 + - + +
1538 LEU* 1.3 73.8 - - - +
1558 SER* 1.4 64.3 + - - +
1568 GLY 5.1 0.4 + - - -
1598 VAL 4.0 1.5 - - - +
1608 THR* 3.2 3.8 - - - +
1618 HIS* 2.7 51.2 + - + +
3008 SER* 3.0 29.3 + - - +
3018 GLY* 4.0 4.5 + - - -
3398 VAL* 4.2 9.3 - - - +
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Residues in contact with SER 155 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1538 LEU* 5.1 3.6 - - - -
1548 ASP* 1.4 76.7 + - - +
1568 GLY* 1.3 60.3 + - - +
1598 VAL 3.6 4.7 + - - -
1608 THR* 2.6 28.0 + - - +
1808 LEU 4.6 0.5 + - - -
1818 ALA* 4.5 2.3 - - - +
2618 LEU* 4.8 4.3 - - - +
2748 ILE* 5.5 1.5 - - - +
3008 SER 3.1 8.5 + - - -
3018 GLY* 3.2 13.7 - - - -
3038 THR* 3.1 37.8 + - - +
3048 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