Contacts of the helix formed by residues 1040 - 1055 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038I ALA 4.3 0.2 - - - -
1039I ALA* 1.3 77.7 - - - +
1041I MET* 1.3 65.1 + - - +
1042I ARG* 3.7 14.0 - - - +
1043I GLU* 2.7 31.4 + - - +
1044I ARG* 3.0 21.3 + - - +
1246T ARG* 5.8 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1041 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983I ALA* 4.9 10.1 - - + +
1039I ALA 3.6 1.0 + - - -
1040I SER* 1.3 72.7 - - - +
1042I ARG* 1.3 63.2 + - - +
1044I ARG* 3.3 8.5 + - - +
1045I ILE* 2.9 44.3 + - + +
1243T GLU* 3.5 48.9 - - + +
1246T ARG* 3.7 58.4 - - + +
1247T MET* 3.6 19.3 - - + -
1250T GLN* 3.9 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1042 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040I SER* 3.1 9.6 - - - +
1041I MET* 1.3 80.6 - - - +
1043I GLU* 1.3 65.2 + - + +
1045I ILE* 3.5 2.8 + - - +
1046I GLU* 3.2 65.1 + - - +
1250T GLN* 3.7 29.4 + - - +
1252T ASN* 5.3 7.9 - - - +
1255T MET* 4.8 18.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1043 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010I PHE* 3.3 32.2 - - + +
1035I VAL* 5.9 0.2 - - - -
1039I ALA* 4.7 7.8 - - + +
1040I SER* 2.7 33.1 + - - +
1041I MET 3.2 0.4 - - - -
1042I ARG* 1.3 80.9 + - + +
1044I ARG* 1.3 65.0 + - - +
1046I GLU* 3.5 3.7 + - - +
1047I PHE* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1044 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982I SER* 4.6 9.4 + - - -
983I ALA* 4.0 22.2 - - + +
984I ALA 4.4 5.6 - - - +
1035I VAL* 3.4 28.1 + - + +
1036I ASN 2.6 34.1 + - - -
1037I GLU* 4.1 6.5 + - - +
1039I ALA* 3.2 26.4 + - + +
1040I SER 3.0 12.6 + - - +
1041I MET* 3.9 6.7 - - - +
1043I GLU* 1.3 77.7 - - - +
1045I ILE* 1.3 60.8 + - - +
1047I PHE* 3.8 9.8 - - + +
1048I LEU* 3.1 36.8 + - + +
1073I GLN 4.5 6.3 + - - -
1075I THR* 3.3 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1045 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983I ALA* 3.9 12.8 - - + -
987I TYR* 3.2 53.2 - - + +
1041I MET* 2.9 49.8 + - + +
1042I ARG* 4.0 3.6 - - - +
1044I ARG* 1.3 74.9 - - - +
1046I GLU* 1.3 59.8 + - - +
1047I PHE 3.1 1.1 - - - -
1048I LEU* 3.1 6.8 + - - +
1049I ASN* 2.9 38.2 + - - +
1247T MET* 4.6 2.2 - - + -
1250T GLN* 3.8 19.5 - - + +
1255T MET* 3.5 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1046 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010I PHE* 3.5 22.2 - - + -
1042I ARG* 3.2 43.9 + - - +
1043I GLU* 3.9 6.4 - - - +
1044I ARG 3.4 0.2 - - - -
1045I ILE* 1.3 77.0 - - - +
1047I PHE* 1.3 61.1 + - - +
1049I ASN* 4.1 3.0 - - + +
1050I GLU* 3.3 29.0 + - - +
1255T MET* 4.2 19.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1047 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I 741 3.6 31.5 - + - -
1010I PHE* 3.4 41.0 - + + -
1033I LYS* 4.1 10.5 - - + -
1035I VAL* 3.1 37.7 - - + -
1043I GLU 3.1 17.3 + - - +
1044I ARG* 3.8 5.6 - - + +
1045I ILE 3.1 0.2 - - - -
1046I GLU* 1.3 78.5 - - - +
1048I LEU* 1.3 78.1 + - + +
1050I GLU* 3.6 4.3 + - - +
1051I ALA* 3.4 19.4 + - + +
1075I THR* 4.6 6.1 - - + -
1077I VAL* 3.1 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1048 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983I ALA* 4.2 5.8 - - + -
984I ALA* 3.8 30.5 - - + +
987I TYR* 4.2 18.8 - - + +
988I VAL* 4.0 24.1 - - + +
1044I ARG* 3.1 34.8 + - + +
1045I ILE* 3.1 5.5 + - - +
1047I PHE* 1.3 101.4 - - + +
1049I ASN* 1.3 59.6 + - - +
1051I ALA* 3.4 8.0 + - + +
1052I SER* 3.1 26.3 + - - -
1068I VAL* 5.5 2.9 - - + -
1075I THR* 4.4 11.4 - - + -
1077I VAL* 4.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1049 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987I TYR* 3.6 28.4 + - - +
1045I ILE* 2.9 20.2 + - - +
1046I GLU* 4.1 4.9 - - + +
1048I LEU* 1.3 79.1 + - - +
1050I GLU* 1.3 59.3 + - - +
1051I ALA 3.1 0.2 - - - -
1052I SER* 2.8 26.7 + - - -
1053I VAL* 3.3 14.2 + - - +
1254T LYS 4.5 3.1 - - - +
1255T MET* 3.2 38.8 - - + +
1261T GLU* 5.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1050 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I 741 3.5 33.0 - - + -
1009I SER* 5.1 1.6 + - - -
1010I PHE* 3.9 18.0 - - - -
1046I GLU* 3.3 18.5 + - - +
1047I PHE 3.7 6.5 - - - +
1049I ASN* 1.3 80.9 - - - +
1051I ALA* 1.3 57.1 + - - +
1053I VAL* 2.9 24.8 - - + +
1054I MET* 3.9 8.3 - - - +
1153I ASP* 4.5 5.7 - - - +
1154I PHE* 4.8 3.6 + - - +
1155I GLY* 3.4 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1051 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I 741 4.3 11.2 - - - +
1047I PHE* 3.4 11.7 + - + +
1048I LEU* 3.4 12.1 + - + +
1049I ASN 3.1 0.8 - - - -
1050I GLU* 1.3 77.4 - - - +
1052I SER* 1.3 59.9 + - - +
1053I VAL 3.2 0.9 - - - -
1054I MET* 3.0 29.2 + - - +
1055I LYS* 3.3 10.1 + - - +
1065I LEU* 4.0 23.0 - - + +
1068I VAL* 5.6 4.5 - - + -
1077I VAL* 4.9 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1052 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987I TYR 3.8 12.0 + - - -
988I VAL* 5.6 0.5 - - - +
1048I LEU 3.1 13.8 + - - -
1049I ASN* 2.8 19.4 + - - -
1051I ALA* 1.3 76.2 - - - +
1053I VAL* 1.3 60.7 + - - +
1055I LYS* 3.1 47.5 + - - +
1056I GLU* 4.6 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1053 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049I ASN 3.3 6.8 + - - +
1050I GLU* 2.9 31.4 - - - +
1052I SER* 1.3 76.7 - - - +
1054I MET* 1.3 67.8 + - - +
1056I GLU* 3.5 18.7 + - - +
1057I PHE* 3.7 19.8 - - + -
1131I PHE* 4.4 22.8 - - + -
1154I PHE* 4.8 20.6 - - + +
1157I THR* 5.7 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1054 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I 741 3.9 23.3 - - + -
1050I GLU 3.9 14.1 - - - +
1051I ALA* 3.0 12.1 - - - +
1053I VAL* 1.3 76.8 - - + +
1055I LYS* 1.3 56.0 + - - +
1057I PHE* 2.6 45.4 + - - +
1062I VAL* 5.5 0.4 - - - -
1063I VAL 3.9 14.8 - - - +
1065I LEU* 4.2 16.7 + - + -
1079I MET* 3.7 26.5 - - + +
1152I GLY 3.6 17.0 - - - +
1154I PHE* 3.4 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1055 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
988I VAL* 4.5 4.0 - - - +
989I PRO* 2.7 40.6 - - + +
992I TRP* 3.1 63.8 - - + +
1051I ALA 3.3 4.9 + - - +
1052I SER* 3.1 49.1 + - - +
1054I MET* 1.3 74.2 - - - +
1056I GLU* 1.3 71.1 + - + +
1057I PHE 3.1 8.2 + - - +
1058I ASN* 5.3 1.7 - - - +
1065I LEU* 4.9 8.2 - - + +
1068I VAL* 6.2 2.1 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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