Contacts of the helix formed by residues 1040 - 1055 (chain D) in PDB entry 3F5P
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 SER1040 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1038D ALA 4.3 0.2 - - - -
1039D ALA* 1.3 78.7 - - - +
1041D MET* 1.3 58.2 + - - +
1042D ARG* 3.2 11.3 + - - +
1043D GLU* 2.8 39.6 + - - +
1044D ARG* 3.0 24.8 + - - -
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Residues in contact with MET1041 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243C GLU* 3.7 33.0 - - + +
1246C ARG* 3.6 41.5 - - + +
1247C MET* 3.7 44.2 - - + -
1250C GLN* 4.1 12.8 - - - +
982D SER* 5.5 0.7 - - - -
983D ALA* 4.4 10.8 - - + +
1040D SER* 1.3 71.4 - - - +
1042D ARG* 1.3 57.0 + - - +
1044D ARG* 3.4 8.6 + - - +
1045D ILE* 2.7 53.9 + - + +
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Residues in contact with ARG1042 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1250C GLN* 3.7 26.6 - - + +
1251C TYR* 6.5 0.9 - - - -
1252C ASN* 5.3 6.5 - - - +
1255C MET* 4.5 19.2 - - - +
1040D SER* 3.2 8.7 + - - +
1041D MET* 1.3 74.6 - - - +
1043D GLU* 1.3 79.7 + - + +
1045D ILE* 2.8 17.0 + - - +
1046D GLU* 2.9 41.1 + - - +
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Residues in contact with GLU1043 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010D PHE* 3.6 24.8 - - + -
1039D ALA* 4.8 7.2 - - + -
1040D SER* 2.8 44.9 + - - +
1042D ARG* 1.3 84.9 + - - +
1044D ARG* 1.3 64.4 + - - +
1046D GLU* 3.4 4.5 + - - +
1047D PHE* 3.0 24.5 + - - +
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Residues in contact with ARG1044 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982D SER* 5.1 7.1 - - - -
983D ALA* 4.2 19.7 - - + +
984D ALA* 4.7 6.7 - - - +
1035D VAL* 4.4 19.7 + - + +
1036D ASN 2.7 30.5 + - - -
1037D GLU* 3.2 21.6 + - - +
1039D ALA* 2.7 26.5 + - + +
1040D SER 3.0 11.2 + - - +
1041D MET* 3.8 7.6 - - - +
1043D GLU* 1.3 79.7 - - - +
1045D ILE* 1.3 54.0 + - - +
1047D PHE* 3.3 9.8 + - + +
1048D LEU* 2.6 47.7 + - + +
1073D GLN 5.5 1.4 + - - -
1075D THR* 4.1 18.6 + - - +
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Residues in contact with ILE1045 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247C MET* 4.5 0.9 - - + -
1250C GLN* 3.5 24.0 - - + +
1255C MET* 3.8 26.9 - - + +
983D ALA* 3.7 15.9 - - + -
987D TYR* 3.4 38.8 - - + +
1041D MET* 2.7 42.7 + - + +
1042D ARG* 2.8 8.1 + - - +
1044D ARG* 1.3 69.4 - - - +
1046D GLU* 1.3 64.6 + - - +
1048D LEU* 3.5 8.9 + - - +
1049D ASN* 3.3 31.3 + - - +
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Residues in contact with GLU1046 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1255C MET* 4.6 19.2 - - + -
1010D PHE* 3.8 20.6 - - - -
1042D ARG* 2.9 34.4 + - - +
1043D GLU* 3.8 5.2 - - - +
1045D ILE* 1.3 76.0 - - - +
1047D PHE* 1.3 63.8 + - - +
1049D ASN* 3.1 17.9 + - + +
1050D GLU* 3.1 14.5 + - - +
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Residues in contact with PHE1047 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D 741 3.2 32.4 - + - -
1010D PHE* 2.8 50.6 - + + -
1033D LYS* 3.8 12.8 - - + -
1035D VAL* 3.5 27.1 - - + -
1043D GLU 3.0 18.2 + - - +
1044D ARG* 3.4 7.9 - - + +
1046D GLU* 1.3 76.7 - - - +
1048D LEU* 1.3 80.4 + - + +
1050D GLU* 3.6 4.8 + - - +
1051D ALA* 3.4 19.3 + - + +
1075D THR* 5.4 0.4 - - + -
1077D VAL* 3.1 37.2 - - + -
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Residues in contact with LEU1048 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983D ALA* 4.3 13.9 - - + -
984D ALA* 4.6 9.9 - - - -
987D TYR* 4.3 19.3 - - + +
988D VAL* 4.1 30.1 - - + -
1044D ARG* 2.6 49.3 + - + +
1045D ILE* 3.5 10.8 - - - +
1046D GLU 3.3 0.2 - - - -
1047D PHE* 1.3 95.2 - - + +
1049D ASN* 1.3 53.1 + - - +
1051D ALA* 2.9 11.0 + - - +
1052D SER* 2.6 35.0 + - - -
1068D VAL* 5.4 2.7 - - + -
1075D THR* 4.7 12.6 - - + -
1077D VAL* 6.0 0.2 - - + -
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Residues in contact with ASN1049 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254C LYS 4.8 2.2 - - - +
1255C MET* 3.6 30.1 - - + +
1261C GLU* 5.7 1.8 + - - -
987D TYR* 4.3 22.8 + - - +
1045D ILE* 3.3 20.8 + - - +
1046D GLU* 3.1 11.7 + - + +
1048D LEU* 1.3 79.3 - - - +
1050D GLU* 1.3 57.8 + - - +
1052D SER* 3.0 29.3 + - - -
1053D VAL* 3.5 13.7 + - - +
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Residues in contact with GLU1050 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D 741 3.7 28.4 - - + -
1010D PHE* 3.8 20.4 - - - -
1046D GLU* 3.1 11.5 + - - +
1047D PHE 3.7 9.0 - - - +
1048D LEU 3.1 0.2 - - - -
1049D ASN* 1.3 73.2 - - - +
1051D ALA* 1.3 63.8 + - - +
1052D SER 3.1 1.3 - - - -
1053D VAL* 3.1 20.7 + - - +
1054D MET* 3.7 12.0 + - + +
1153D ASP* 4.5 4.5 - - - +
1154D PHE* 4.0 9.5 + - - +
1155D GLY* 3.2 38.6 + - - +
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Residues in contact with ALA1051 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D 741 4.6 11.0 - - - +
1047D PHE* 3.4 10.9 + - + +
1048D LEU* 2.9 11.7 + - + +
1050D GLU* 1.3 75.0 - - - +
1052D SER* 1.3 64.2 + - - +
1053D VAL 3.0 2.9 + - - -
1054D MET* 3.4 26.0 + - - +
1055D LYS* 3.4 8.5 + - - +
1065D LEU* 3.6 25.5 - - + +
1068D VAL* 5.9 3.4 - - + -
1077D VAL* 4.7 8.3 - - + -
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Residues in contact with SER1052 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987D TYR 4.9 8.5 + - - -
1048D LEU 2.6 15.3 + - - -
1049D ASN* 3.0 32.4 + - - -
1050D GLU 3.1 0.2 - - - -
1051D ALA* 1.3 73.6 - - - +
1053D VAL* 1.3 58.8 + - - +
1055D LYS* 4.3 11.5 - - - +
1056D GLU* 4.6 2.4 + - - +
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Residues in contact with VAL1053 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049D ASN 3.7 13.7 - - - +
1050D GLU* 3.1 10.0 + - - +
1051D ALA 3.0 0.6 - - - -
1052D SER* 1.3 76.5 - - - +
1054D MET* 1.3 68.9 - - - +
1056D GLU* 3.1 23.2 + - - +
1057D PHE* 3.5 27.0 + - + -
1131D PHE* 4.0 21.8 - - + -
1154D PHE* 5.5 6.7 - - + +
1157D THR* 4.8 9.2 - - - +
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Residues in contact with MET1054 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D 741 3.4 35.7 - - + +
1050D GLU* 3.7 11.0 - - + +
1051D ALA* 3.4 21.5 - - - +
1053D VAL* 1.3 74.1 - - - +
1055D LYS* 1.3 54.4 + - - +
1056D GLU 2.6 1.4 + - - -
1057D PHE* 2.4 50.7 + - - +
1063D VAL 4.6 5.8 - - - +
1065D LEU* 4.0 18.6 - - + +
1079D MET* 3.5 19.1 - - + -
1152D GLY 4.3 7.2 - - - +
1153D ASP* 5.4 0.7 - - - -
1154D PHE* 3.7 41.3 - - + +
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Residues in contact with LYS1055 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992D TRP* 3.2 60.2 - - + +
1051D ALA 3.4 11.0 + - - +
1052D SER* 4.3 9.2 - - - +
1053D VAL 3.3 0.8 + - - -
1054D MET* 1.3 77.2 - - - +
1056D GLU* 1.3 63.4 + - - +
1057D PHE 4.0 5.9 - - - +
1058D ASN* 5.6 1.0 - - - +
1065D LEU* 4.7 4.2 - - + +
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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