Contacts of the strand formed by residues 999 - 1004 (chain A) in PDB entry 4OUL
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 ALA 999 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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998A VAL* 1.3 75.5 - - - +
1000A PHE* 1.3 63.6 + - - +
1024A ASN* 3.9 3.3 - - - +
1025A ASN* 3.2 2.9 + - - -
1026A LEU* 2.6 51.5 + - + +
1029A THR* 5.4 1.9 + - - -
1121A GLY 3.2 7.2 - - - +
1122A TYR* 3.7 13.9 - - + -
1044B THR* 4.5 5.8 - - + -
1091B ILE* 4.1 20.6 - - + -
1124B LEU* 6.2 0.7 - - + -
1125B TYR* 4.2 9.6 - - + -
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Residues in contact with PHE1000 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999A ALA* 1.3 75.3 - - - +
1001A SER* 1.3 65.6 + - - +
1002A ALA 4.6 1.6 - - - -
1022A LEU* 5.1 0.7 - - + -
1024A ASN* 3.2 7.6 - - - +
1025A ASN* 3.2 23.3 - - - +
1029A THR* 4.2 4.7 - - - +
1030A PHE* 3.5 41.3 - + + -
1037A PHE* 3.6 37.7 - + + -
1047A PHE* 3.9 7.4 - + - -
1119A PHE* 3.7 38.1 - + - -
1120A SER* 3.2 13.1 - - - -
1121A GLY* 2.9 54.1 + - - +
1091B ILE* 4.0 4.4 - - - +
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Residues in contact with SER1001 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000A PHE* 1.3 75.1 - - - +
1002A ALA* 1.3 57.9 + - - +
1022A LEU* 3.4 5.6 - - - +
1023A LEU* 2.5 52.6 + - - +
1024A ASN 3.1 7.4 + - - -
1118A THR* 5.6 1.4 - - - +
1119A PHE 3.6 0.9 - - - -
1120A SER* 2.7 22.3 + - - -
1089B HIS* 4.5 0.7 + - - -
1090B ALA* 4.1 2.8 - - - -
1091B ILE* 3.3 37.0 + - - -
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Residues in contact with ALA1002 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000A PHE* 5.0 0.4 - - + -
1001A SER* 1.3 75.3 + - - +
1003A ALA* 1.3 61.1 + - - +
1019A PHE* 3.6 29.2 - - + -
1021A LEU 3.5 5.2 - - - +
1022A LEU* 3.7 18.4 - - + -
1023A LEU* 4.8 2.2 - - - -
1030A PHE* 3.9 13.2 - - + -
1118A THR* 3.2 7.8 - - - +
1119A PHE 2.7 36.8 + - - +
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Residues in contact with ALA1003 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002A ALA* 1.3 77.2 - - - +
1004A ARG* 1.3 58.3 + - - +
1019A PHE* 3.5 7.7 - - - -
1020A ASP* 3.2 26.7 + - - +
1021A LEU* 3.1 18.3 + - + +
1023A LEU* 4.3 7.0 - - + -
1115A LYS* 3.9 37.9 - - + -
1117A SER 3.2 11.4 - - - +
1118A THR* 4.3 6.3 - - + -
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Residues in contact with ARG1004 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003A ALA* 1.3 71.4 - - - +
1005A THR* 1.3 62.2 + - - +
1006A SER* 2.7 49.6 + - - +
1007A ASN 3.3 10.3 + - - -
1008A LEU* 3.6 36.3 - - - +
1017A ILE* 4.5 3.4 - - + -
1018A VAL* 2.6 52.5 + - - +
1019A PHE* 3.8 21.6 - - + +
1020A ASP* 3.8 11.7 + - - +
1051A MET* 5.9 0.2 - - - -
1109A ILE* 4.3 13.0 - - + -
1110A TYR 4.6 0.7 - - - +
1111A GLY* 3.5 13.9 - - - -
1112A SER 3.7 6.1 + - - +
1115A LYS* 4.3 9.4 - - - -
1117A SER* 3.0 24.2 + - - +
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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