Contacts of the helix formed by residues 1041 - 1055 (chain B) 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 GLY1041 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579B HIS* 3.7 16.6 - - - -
1037B GLU* 3.0 14.8 + - - -
1039B GLY 3.1 2.6 + - - -
1040B GLN* 1.3 80.4 - - - +
1042B LEU* 1.3 63.9 + - - +
1043B HIS 3.4 2.2 - - - -
1044B THR* 3.5 10.3 + - - -
1045B LYS* 3.1 29.5 + - - +
1190B ILE* 4.4 8.4 - - - +
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Residues in contact with LEU1042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033B HIS* 3.9 10.8 - - + -
1035B GLY* 3.7 24.9 - - - -
1036B THR 3.5 20.2 - - - +
1037B GLU* 2.9 5.4 + - - +
1040B GLN* 3.5 21.6 - - + +
1041B GLY* 1.3 74.8 - - - +
1043B HIS* 1.3 61.5 + - - +
1045B LYS* 3.3 5.8 + - - +
1046B MET* 2.9 44.0 + - + +
1077B THR* 4.2 0.7 - - + -
1082B SER* 3.7 27.1 - - - +
1083B THR* 3.9 35.4 - - - +
1086B TYR* 4.4 0.9 - - + -
4003B MTE 4.1 1.1 - - - +
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Residues in contact with HIS1043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B HIS* 6.4 1.1 - - + -
580B LEU* 4.3 7.0 - - + -
792B LYS 4.4 9.3 + - - -
1033B HIS* 2.9 36.4 + + - -
1035B GLY 3.7 11.2 - - - -
1036B THR 4.6 0.7 - - - -
1037B GLU* 3.3 39.7 + - + +
1042B LEU* 1.3 73.6 - - + +
1044B THR* 1.3 66.5 + - - +
1046B MET* 3.1 1.4 + - - +
1047B VAL* 2.9 29.5 + - - +
1063B ILE* 3.6 39.8 - - + +
1064B SER 5.6 1.3 - - - -
1065B GLU* 4.7 6.8 - - - -
1066B THR* 4.0 10.6 + - - -
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Residues in contact with THR1044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B LEU* 3.9 11.4 - - + +
578B PRO 3.9 16.4 - - - +
579B HIS* 3.4 16.6 + - - -
580B LEU* 2.8 44.9 + - + +
1037B GLU* 4.7 0.2 + - - -
1041B GLY* 3.5 12.5 + - - -
1042B LEU 3.3 0.2 - - - -
1043B HIS* 1.3 80.0 - - - +
1045B LYS* 1.3 56.8 + - - +
1047B VAL* 3.3 3.1 + - - +
1048B GLN* 3.0 43.3 + - - +
1187B ASN* 4.3 8.1 - - - +
1190B ILE* 4.9 3.6 - - + -
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Residues in contact with LYS1045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040B GLN 5.2 1.9 + - - +
1041B GLY 3.1 19.0 + - - +
1042B LEU* 3.6 6.1 - - - +
1044B THR* 1.3 81.2 - - - +
1046B MET* 1.3 67.3 + - + +
1048B GLN* 3.2 18.0 + - - +
1049B VAL* 2.9 32.6 + - - +
1083B THR* 3.6 30.4 + - + +
1186B LEU* 4.3 19.5 - - + +
1187B ASN* 4.4 8.5 - - + -
1190B ILE* 4.1 23.4 - - + +
1191B ASP* 2.6 34.8 + - - -
1194B GLN* 5.6 0.4 - - - +
1257B LYS 5.6 2.4 + - - -
1259B VAL* 4.1 11.9 - - - +
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Residues in contact with MET1046 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031B VAL* 5.2 1.0 - - + +
1033B HIS* 3.6 23.3 - - + +
1042B LEU* 2.9 27.7 + - + +
1043B HIS 3.1 4.7 + - - +
1045B LYS* 1.3 79.3 - - + +
1047B VAL* 1.3 61.7 + - - +
1049B VAL* 3.6 7.8 - - + +
1050B ALA* 2.9 29.1 + - - +
1063B ILE* 3.8 15.5 - - + -
1083B THR* 3.8 29.2 - - + +
1086B TYR* 3.4 15.5 - - - +
1087B GLY* 3.3 41.7 - - - +
1090B VAL* 4.1 13.1 - - + +
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Residues in contact with VAL1047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B LEU* 6.2 0.4 - - + -
580B LEU* 3.6 26.0 - - + -
1031B VAL* 6.1 0.2 - - - -
1043B HIS 2.9 21.2 + - - +
1044B THR 3.6 4.5 - - - +
1046B MET* 1.3 73.2 - - - +
1048B GLN* 1.3 60.7 + - + +
1050B ALA* 3.9 5.9 - - - +
1051B SER* 2.8 30.0 + - - -
1058B ILE* 3.7 28.9 - - + +
1061B ILE* 3.9 30.0 - - + +
1063B ILE* 4.0 25.8 - - + +
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Residues in contact with GLN1048 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B THR* 2.8 50.7 + - - +
573B VAL* 3.5 20.0 + - + +
575B ARG 3.8 4.4 + - - -
577B LEU* 3.9 18.4 - - + +
1044B THR* 3.0 21.5 + - - +
1045B LYS* 3.2 17.3 + - - +
1047B VAL* 1.3 77.3 - - - +
1049B VAL* 1.3 61.4 + - + +
1051B SER* 3.6 2.6 + - - -
1052B LYS* 3.2 16.1 + - - +
1058B ILE* 4.4 4.3 - - + -
1186B LEU* 3.5 15.8 + - + +
1187B ASN* 2.9 35.9 + - - +
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Residues in contact with VAL1049 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B VAL* 4.5 1.6 - - + -
1045B LYS 2.9 21.1 + - - +
1046B MET* 3.6 15.9 - - + +
1048B GLN* 1.3 74.3 - - + +
1050B ALA* 1.3 67.7 + - - +
1052B LYS* 3.0 4.0 + - - +
1053B ALA* 3.0 21.7 + - - +
1087B GLY* 3.8 23.3 - - - +
1090B VAL* 4.5 6.5 - - + -
1091B TYR* 4.7 7.6 - - + +
1186B LEU* 3.7 25.1 - - + -
1253B ILE* 4.4 9.4 - - + -
1254B TYR* 3.9 30.2 + - + +
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Residues in contact with ALA1050 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031B VAL* 4.3 16.6 - - + -
1046B MET 2.9 21.7 + - - +
1047B VAL 3.9 0.7 - - - +
1049B VAL* 1.3 73.1 - - - +
1051B SER* 1.3 63.3 + - - +
1054B LEU* 3.0 33.0 + - + +
1061B ILE* 3.6 17.7 - - + -
1090B VAL* 3.9 15.5 - - + -
1094B CYS* 4.0 17.5 - - - -
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Residues in contact with SER1051 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570B GLU 3.3 18.2 + - - +
572B THR* 5.1 0.7 + - - -
1047B VAL 2.8 18.4 + - - -
1048B GLN 3.7 4.0 - - - -
1050B ALA* 1.3 77.8 - - - +
1052B LYS* 1.3 56.6 + - - +
1055B LYS* 2.9 23.9 + - - -
1056B ILE* 2.7 32.4 + - - +
1058B ILE* 3.4 23.4 + - - +
1061B ILE* 3.3 14.3 - - - +
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Residues in contact with LYS1052 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567B GLN* 5.5 0.8 + - - -
571B ASP* 2.6 40.6 + - - +
573B VAL* 3.5 26.5 - - + -
1048B GLN 3.2 10.5 + - - +
1049B VAL 3.0 8.5 + - - +
1051B SER* 1.3 77.6 + - - +
1053B ALA* 1.3 65.9 + - - +
1055B LYS* 3.2 23.8 + - - +
1254B TYR* 3.4 40.6 - - + +
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Residues in contact with ALA1053 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049B VAL 3.0 15.1 + - - +
1050B ALA* 4.0 1.6 - - - +
1052B LYS* 1.3 77.1 - - - +
1054B LEU* 1.3 60.1 + - - +
1055B LYS* 4.5 7.2 + - - +
1091B TYR* 4.0 9.6 - - + -
1094B CYS* 3.8 25.1 - - + -
1095B GLN* 3.9 15.6 + - - +
1098B LEU* 3.2 22.7 - - - +
1254B TYR* 3.5 15.6 + - - +
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Residues in contact with LEU1054 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021B ILE* 5.7 2.5 - - + -
1023B VAL* 5.8 0.7 - - + -
1029B VAL* 4.5 18.6 - - + -
1050B ALA* 3.0 24.7 + - + +
1053B ALA* 1.3 75.3 - - - +
1055B LYS* 1.3 70.8 + - - +
1056B ILE* 3.8 36.1 - - + +
1061B ILE* 4.5 4.3 - - + -
1094B CYS* 3.6 47.1 - - + +
1097B ILE* 4.4 9.9 - - + -
1098B LEU* 4.0 23.0 - - + +
1113B TRP* 4.3 21.0 - - + -
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Residues in contact with LYS1055 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570B GLU* 4.2 8.7 - - - +
1051B SER 2.9 10.1 + - - -
1052B LYS* 3.2 15.4 + - - +
1053B ALA 4.5 5.4 + - - +
1054B LEU* 1.3 81.6 - - - +
1056B ILE* 1.3 64.4 + - - +
1098B LEU* 6.4 1.3 - - + -
1105B LYS* 6.1 3.6 - - - +
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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