Contacts of the helix formed by residues 1028 - 1050 (chain D) in PDB entry 6X34
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 ASP1028 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020D ARG* 4.6 16.4 - - + -
1026D LEU* 4.6 4.4 - - - -
1027D LEU* 1.3 77.5 - - - +
1029D GLU* 1.3 61.3 + - - +
1030D ALA* 3.5 1.1 - - + +
1031D THR* 3.7 24.4 - - - +
1032D LYS* 3.2 25.1 + - - +
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Residues in contact with GLU1029 (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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1026D LEU 4.8 2.2 + - - +
1027D LEU 4.0 2.8 + - - -
1028D ASP* 1.3 70.3 - - - +
1030D ALA* 1.3 61.8 + - - +
1032D LYS* 3.4 5.3 + - - +
1033D ARG* 2.9 29.8 + - - +
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Residues in contact with ALA1030 (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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1028D ASP* 4.5 1.5 - - + +
1029D GLU* 1.3 78.4 - - - +
1031D THR* 1.3 56.6 + - - +
1033D ARG* 3.3 6.3 + - - +
1034D SER* 2.9 29.7 + - - -
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Residues in contact with THR1031 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993D HIS* 4.9 9.2 + - - -
1028D ASP* 3.7 23.4 + - - +
1029D GLU 3.3 0.4 - - - -
1030D ALA* 1.3 77.8 - - - +
1032D LYS* 1.3 59.2 + - - +
1034D SER* 3.3 7.4 + - - -
1035D ASN* 2.9 30.3 + - - +
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Residues in contact with LYS1032 (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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993D HIS* 6.1 0.2 - - - -
1026D LEU* 5.9 5.6 - - - -
1028D ASP 3.2 17.9 + - - +
1029D GLU* 3.7 5.8 - - - +
1030D ALA 3.3 0.2 - - - -
1031D THR* 1.3 80.3 - - - +
1033D ARG* 1.3 57.1 + - - +
1035D ASN* 3.3 6.3 + - - +
1036D ARG* 2.9 31.1 + - - +
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Residues in contact with ARG1033 (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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1029D GLU 2.9 18.0 + - - +
1030D ALA* 3.7 6.7 - - - +
1032D LYS* 1.3 75.8 - - - +
1034D SER* 1.3 58.0 + - - +
1036D ARG* 3.3 5.4 + - - +
1037D ASP* 2.9 32.6 + - - +
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Residues in contact with SER1034 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030D ALA 2.9 16.5 + - - -
1031D THR* 3.7 7.9 - - - -
1033D ARG* 1.3 78.1 - - - +
1035D ASN* 1.3 57.6 + - - +
1037D ASP* 4.7 3.1 - - - -
1038D SER* 2.9 38.4 + - - -
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Residues in contact with ASN1035 (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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985D VAL 4.6 1.2 - - - +
989D ALA* 3.5 19.8 - - + +
993D HIS* 3.5 32.1 - - + +
1031D THR 2.9 17.6 + - - +
1032D LYS* 3.8 6.3 - - - +
1034D SER* 1.3 77.6 - - - +
1036D ARG* 1.3 57.8 + - - +
1039D LEU* 3.2 28.5 - - - +
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Residues in contact with ARG1036 (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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982D THR* 5.6 2.6 - - - +
985D VAL* 4.8 2.3 - - - +
986D ASP* 5.0 20.6 - - + +
989D ALA* 5.4 0.2 - - - -
1032D LYS 2.9 18.0 + - - +
1033D ARG* 3.8 5.8 - - - +
1034D SER 3.2 0.2 - - - -
1035D ASN* 1.3 78.4 - - - +
1037D ASP* 1.3 56.7 + - - +
1040D CYS* 3.3 22.7 - - - +
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Residues in contact with ASP1037 (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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1033D ARG 2.9 17.0 + - - +
1034D SER* 4.1 2.9 - - - +
1036D ARG* 1.3 78.3 - - - +
1038D SER* 1.3 61.4 + - - +
1040D CYS* 3.3 3.8 + - - +
1041D GLN* 2.9 29.4 + - - +
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Residues in contact with SER1038 (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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1034D SER* 2.9 21.6 + - - +
1037D ASP* 1.3 74.5 - - - +
1039D LEU* 1.3 57.3 + - - +
1041D GLN* 3.3 5.5 + - - +
1042D ALA* 2.9 30.1 + - - +
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Residues in contact with LEU1039 (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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928D THR* 5.8 0.9 - - - +
985D VAL* 4.7 8.7 - - + +
988D LEU* 6.3 1.1 - - + -
989D ALA* 4.7 11.2 - - + +
1034D SER 4.1 0.4 + - - -
1035D ASN* 3.2 25.2 + - - +
1037D ASP 3.4 0.4 - - - -
1038D SER* 1.3 77.8 - - - +
1040D CYS* 1.3 56.6 + - - +
1042D ALA* 3.3 6.1 + - - +
1043D VAL* 2.9 29.8 + - - +
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Residues in contact with CYS1040 (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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981D GLN 5.4 0.7 - - - +
982D THR* 5.3 7.6 - - - -
985D VAL* 3.7 23.4 - - + +
1036D ARG 3.3 21.7 + - - +
1037D ASP* 3.3 5.2 + - - +
1038D SER 3.3 0.4 - - - -
1039D LEU* 1.3 79.3 - - - +
1041D GLN* 1.3 57.3 + - - +
1043D VAL* 3.3 3.5 + - - +
1044D ARG* 2.9 30.0 + - - +
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Residues in contact with GLN1041 (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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1037D ASP 2.9 16.9 + - - +
1038D SER* 3.7 7.2 - - - +
1040D CYS* 1.3 77.5 - - - +
1042D ALA* 1.3 56.5 + - - +
1044D ARG* 3.3 6.5 + - - +
1045D THR* 2.9 30.2 + - - -
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Residues in contact with ALA1042 (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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874D LEU* 5.4 3.8 - - + +
877D ASN* 5.7 5.4 - - + +
878D ILE* 6.0 9.2 - - + +
928D THR* 4.9 13.8 - - + +
1038D SER 2.9 17.0 + - - +
1039D LEU* 3.7 7.0 - - - +
1041D GLN* 1.3 76.7 - - - +
1043D VAL* 1.3 58.3 + - - +
1045D THR* 3.3 5.6 + - - -
1046D LEU* 2.9 30.8 + - - +
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Residues in contact with VAL1043 (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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928D THR* 4.6 12.3 - - + +
932D LEU* 6.0 5.6 - - + -
985D VAL* 5.4 5.6 - - + -
1039D LEU 2.9 17.4 + - - +
1040D CYS* 3.7 7.2 - - - +
1042D ALA* 1.3 75.4 - - - +
1044D ARG* 1.3 58.4 + - - +
1046D LEU* 3.3 6.2 + - - +
1047D LEU* 2.9 30.5 + - - +
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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
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1040D CYS 2.9 18.0 + - - +
1041D GLN* 3.7 6.7 - - - +
1043D VAL* 1.3 77.0 - - - +
1045D THR* 1.3 56.7 + - - +
1047D LEU* 3.3 5.3 + - - +
1048D GLY* 2.9 27.0 + - - -
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Residues in contact with THR1045 (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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877D ASN* 4.2 15.3 - - - -
969D PRO* 4.9 7.2 - - - -
971D ASP* 3.4 29.4 - - - +
1041D GLN 2.9 17.6 + - - -
1042D ALA* 3.8 5.4 - - - -
1043D VAL 3.3 0.2 - - - -
1044D ARG* 1.3 77.3 - - - +
1046D LEU* 1.3 61.6 + - - +
1048D GLY* 5.3 0.2 - - - -
1049D TYR* 3.2 26.9 + - - +
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Residues in contact with LEU1046 (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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870D ILE* 4.3 18.4 - - + +
873D LYS 5.5 0.2 - - - -
874D LEU* 3.7 32.7 - - + +
928D THR* 4.8 7.4 - - + -
1042D ALA 2.9 18.1 + - - +
1043D VAL* 3.8 6.3 - - - +
1045D THR* 1.3 75.2 - - - +
1047D LEU* 1.3 64.1 + - - +
1049D TYR* 4.2 4.2 - - - +
1050D GLY 3.7 13.9 + - - -
1051D TYR 4.2 4.3 - - - +
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Residues in contact with LEU1047 (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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946D ALA* 5.7 0.5 - - - +
1043D VAL 2.9 18.1 + - - +
1044D ARG* 3.9 5.8 - - - +
1046D LEU* 1.3 78.4 - - - +
1048D GLY* 1.3 61.8 + - - +
1049D TYR 3.5 0.3 + - - -
1050D GLY 4.0 2.6 - - - +
1051D TYR 3.5 12.7 - - - +
1052D ASN* 3.3 24.9 + - + +
1053D ILE* 4.3 25.1 - - + +
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Residues in contact with GLY1048 (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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946D ALA* 3.3 25.8 - - - +
971D ASP 3.9 8.5 - - - +
1044D ARG 2.9 15.6 + - - -
1045D THR* 4.2 0.9 - - - -
1047D LEU* 1.3 74.3 - - - +
1049D TYR* 1.3 62.4 + - - +
1052D ASN* 5.8 0.7 - - - -
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Residues in contact with TYR1049 (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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873D LYS* 3.7 28.0 - - + -
946D ALA 3.4 14.8 - - - +
947D GLU* 3.6 15.1 + - - +
971D ASP* 3.4 21.3 + - + +
1045D THR 3.2 19.9 + - - +
1046D LEU 4.2 2.7 - - - +
1047D LEU 3.3 0.4 - - - -
1048D GLY* 1.3 81.4 - - - +
1050D GLY* 1.3 61.7 + - - +
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Residues in contact with GLY1050 (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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869D ARG* 5.4 4.7 - - - -
870D ILE* 4.8 12.1 - - - +
873D LYS* 5.2 1.1 - - - +
941D MET* 4.6 8.2 - - - +
942D ALA 5.0 0.3 + - - -
946D ALA* 4.1 14.4 - - - +
947D GLU* 5.9 0.9 - - - -
1046D LEU 3.7 6.4 + - - -
1047D LEU 4.0 3.1 - - - +
1049D TYR* 1.3 82.6 - - - +
1051D TYR* 1.3 62.7 + - - +
1052D ASN* 3.6 2.8 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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