Contacts of the strand formed by residues 150 - 155 (chain 2) 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 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1422 LEU* 3.8 14.3 - - - +
1492 THR* 1.3 77.4 - - - +
1512 ILE* 1.3 61.5 + - - +
1642 PRO* 3.7 0.5 - - - +
1652 ILE* 2.9 28.9 + - - +
2922 ASP 4.8 0.2 - - - -
2932 LEU* 3.8 13.2 - - - +
2962 ASN* 3.2 20.6 - - - -
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Residues in contact with ILE 151 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1422 LEU* 4.4 0.6 - - - +
1502 GLY* 1.3 74.7 - - - +
1522 VAL* 1.3 64.9 + - - +
1532 LEU 4.0 0.3 + - - -
1622 ASN* 4.5 6.3 - - + +
1632 VAL 3.7 8.7 - - - +
1642 PRO* 3.9 22.2 - - + -
2782 THR* 3.6 29.2 - - + +
2812 SER* 3.6 21.5 - - - +
2822 ILE* 3.7 13.0 - - + -
2932 LEU* 3.4 33.2 - - + +
2962 ASN 2.8 8.4 + - - +
2972 ASN* 3.4 20.2 - - - +
2982 VAL 2.9 23.6 + - - +
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Residues in contact with VAL 152 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1382 ALA* 3.3 41.1 - - + +
1412 SER* 4.3 2.7 - - - -
1422 LEU* 3.8 29.8 - - + +
1512 ILE* 1.3 74.7 - - - +
1532 LEU* 1.3 67.6 + - - +
1542 ASP* 3.6 10.2 + - + -
1612 HIS 4.1 0.2 - - - -
1622 ASN* 3.2 6.5 - - - +
1632 VAL* 2.9 33.4 + - - +
1652 ILE* 4.5 1.3 - - + -
2972 ASN* 5.6 0.2 - - - -
2982 VAL* 3.1 15.3 - - + +
3002 SER* 3.6 24.5 - - - +
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Residues in contact with LEU 153 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512 ILE 4.0 1.2 + - - -
1522 VAL* 1.3 71.7 - - - +
1542 ASP* 1.3 59.2 + - - +
1552 SER* 5.1 2.7 - - - -
1602 THR* 4.4 9.0 - - + -
1612 HIS 3.4 8.5 - - - +
1622 ASN* 3.6 24.7 - - - +
2742 ILE* 3.6 42.2 - - + +
2772 THR* 5.9 0.2 - - + -
2782 THR* 3.9 10.1 - - - +
2972 ASN* 4.5 14.0 - - - +
2982 VAL 2.9 7.8 + - - +
2992 MET* 3.6 34.9 - - + +
3002 SER 3.1 24.1 + - - +
3042 THR* 4.0 13.2 - - + -
3092 ILE* 5.7 4.9 - - + -
3132 MET* 4.5 3.6 - - + -
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Residues in contact with ASP 154 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092 PRO* 5.9 1.9 - - - +
1372 GLN* 4.0 26.2 - - - +
1382 ALA* 4.1 10.7 + - + +
1522 VAL* 3.6 12.5 + - + +
1532 LEU* 1.3 74.1 - - - +
1552 SER* 1.4 64.3 + - - +
1592 VAL 4.0 1.1 - - - +
1602 THR* 3.2 3.9 - - - +
1612 HIS* 2.7 50.4 + - + +
3002 SER* 3.0 30.7 + - - +
3012 GLY* 4.0 5.0 + - - -
3392 VAL* 4.3 9.5 - - - +
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Residues in contact with SER 155 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1532 LEU* 5.1 3.6 - - - -
1542 ASP* 1.4 75.4 + - - +
1562 GLY* 1.3 60.9 + - - +
1592 VAL 3.6 3.8 - - - -
1602 THR* 2.6 27.7 + - - +
1802 LEU 4.6 0.5 + - - -
1812 ALA* 4.5 2.6 - - - +
2612 LEU* 4.8 4.6 - - - +
2742 ILE* 5.5 0.8 - - - +
3002 SER 3.1 8.5 + - - -
3012 GLY* 3.2 13.8 - - - -
3032 THR* 3.1 39.2 + - - +
3042 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