Contacts of the strand formed by residues 1128 - 1134 (chain A) in PDB entry 1FO4
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 SER1128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020A LEU* 4.1 1.0 - - - +
1021A ILE 3.4 4.3 - - - -
1022A HIS* 2.8 33.2 + - - -
1100A ARG* 2.8 21.7 + - - +
1126A SER* 3.3 10.0 + - - -
1127A LEU* 1.3 80.7 - - - +
1129A THR* 1.3 62.7 + - - +
1070B THR 4.7 1.2 + - - -
1072B PRO* 3.7 17.7 - - - +
1130B THR* 3.9 22.0 + - - +
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Residues in contact with THR1129 (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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1020A LEU* 3.5 4.7 - - - +
1021A ILE* 3.0 31.6 + - + +
1093A ALA* 3.3 31.5 - - + +
1096A THR* 3.6 25.0 + - - +
1097A ILE* 3.6 17.9 - - + -
1100A ARG* 4.1 8.1 + - - -
1128A SER* 1.3 76.6 + - - +
1130A THR* 1.3 81.3 + - - +
1130B THR* 4.2 8.8 + - - -
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Residues in contact with THR1130 (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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1019A ALA 3.1 11.9 - - - +
1020A LEU* 4.0 17.7 - - + -
1070A THR 5.8 0.7 - - - +
1092A GLU 5.1 0.2 - - - -
1093A ALA* 3.9 7.5 - - - +
1096A THR* 4.9 2.6 + - - -
1129A THR* 1.3 96.0 + - - +
1131A GLY* 1.3 61.3 + - - +
1132A PHE* 6.1 0.2 - - - +
1020B LEU* 4.4 9.2 - - + -
1100B ARG* 4.8 7.3 + - - -
1126B SER* 5.4 2.3 + - - -
1128B SER* 4.0 36.5 + - - +
1129B THR* 4.4 8.1 + - - -
1130B THR* 4.5 5.4 + - + +
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Residues in contact with GLY1131 (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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1018A GLY* 3.2 4.0 - - - -
1019A ALA 2.8 30.6 + - - +
1089A ALA* 3.4 23.8 - - - -
1092A GLU* 4.5 2.9 - - - -
1093A ALA* 4.0 9.2 - - - +
1130A THR* 1.3 78.3 - - - +
1132A PHE* 1.3 63.0 + - - +
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Residues in contact with PHE1132 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1016A GLN* 3.4 34.3 - - + -
1017A ALA 3.2 31.4 - - - -
1018A GLY* 4.0 8.1 - - - -
1089A ALA* 4.0 4.7 - - - +
1092A GLU* 3.9 19.7 - - - +
1130A THR* 6.1 0.4 - - - +
1131A GLY* 1.3 74.8 - - - +
1133A TYR* 1.3 82.1 + - - +
1134A ARG* 4.6 3.6 - - + -
1124B ARG 3.2 24.7 - - - -
1125B VAL* 4.3 0.2 - - - -
1126B SER* 3.4 46.2 - - - +
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Residues in contact with TYR1133 (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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1016A GLN* 3.2 7.6 - - - +
1017A ALA 3.0 30.1 + - - +
1084A ASP* 4.4 4.7 - - + -
1085A ILE* 3.7 41.5 - - + +
1088A GLN* 3.1 45.6 + - + -
1089A ALA 4.1 2.5 - - - +
1092A GLU* 6.0 0.9 - - + -
1132A PHE* 1.3 83.3 - - - +
1134A ARG* 1.3 71.5 + - - +
1135A THR* 3.5 30.3 - - + +
1136A PRO* 3.6 18.3 - - + +
1151A HIS* 4.3 9.0 + - - -
1251A LYS 4.7 5.2 + - - -
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Residues in contact with ARG1134 (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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1015A ASN 3.7 3.4 - - - -
1016A GLN* 4.7 0.2 - - - +
1132A PHE* 4.6 3.6 - - + -
1133A TYR* 1.3 83.0 - - - +
1135A THR* 1.3 67.4 + - - +
1136A PRO* 3.1 10.2 - - - +
1123B ASP* 3.4 22.9 + - - -
1124B ARG* 3.1 63.3 + - + +
1125B VAL* 4.0 12.7 - - - +
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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