Contacts of the helix formed by residues 1044 - 1058 (chain A) in PDB entry 2XT6
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 THR1044 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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878A TRP* 3.7 11.5 - - - -
1042A PRO* 3.6 0.7 - - - +
1043A SER* 1.3 86.6 - - - +
1045A PRO* 1.4 72.8 - - - +
1046A ALA* 3.9 1.6 + - - +
1047A ASN* 3.1 25.1 + - - +
1048A TYR 3.2 15.9 + - - -
1079A VAL 5.5 2.7 - - - +
1080A SER* 4.0 8.4 + - - -
1094A LEU* 4.3 8.7 - - + +
1121A TYR* 3.7 9.9 - - - +
1139A ARG* 3.8 20.0 - - - +
1141A GLU* 4.2 0.8 + - - -
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Residues in contact with PRO1045 (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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876A ILE 3.4 22.9 - - - +
877A ASP 3.6 3.6 - - - +
878A TRP* 3.4 28.0 - - + +
881A ALA* 3.3 32.9 - - + +
1043A SER 4.7 0.2 - - - +
1044A THR* 1.4 83.5 - - - +
1046A ALA* 1.4 55.2 + - - +
1048A TYR* 3.4 4.4 + - + +
1049A PHE 3.1 21.5 + - - -
1078A ALA* 3.2 33.9 - - + +
1079A VAL 4.2 1.3 - - - -
1080A SER* 3.5 14.4 - - - +
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Residues in contact with ALA1046 (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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1044A THR* 4.6 1.8 - - - +
1045A PRO* 1.4 72.0 - - - +
1047A ASN* 1.4 61.9 + - - +
1049A PHE* 3.1 1.2 + - - +
1050A HIS* 2.9 37.2 + - + -
1080A SER* 3.1 23.7 + - - +
1084A ASP* 3.6 35.7 - - + +
1085A PHE* 3.7 18.6 - - + -
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Residues in contact with ASN1047 (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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1042A PRO* 4.4 3.5 - - + +
1044A THR* 3.1 22.9 + - - +
1046A ALA* 1.4 75.6 - - - +
1048A TYR* 1.3 57.1 + - - +
1050A HIS* 3.5 2.6 + - - +
1051A LEU* 3.0 24.1 + - - +
1089A LYS 4.1 3.1 - - - +
1090A PHE* 3.3 30.0 - - - -
1091A ARG* 2.9 48.5 + - - +
1094A LEU* 4.2 7.7 - - + +
1141A GLU* 2.8 32.6 + - - +
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Residues in contact with TYR1048 (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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878A TRP* 3.3 59.9 - + + -
882A GLU* 2.6 51.0 + - + +
972A LEU* 4.9 0.2 - - - +
1008A LEU* 3.3 22.0 - - + +
1042A PRO* 4.0 10.4 - - + +
1044A THR 3.2 7.2 + - - +
1045A PRO 3.4 9.2 - - - +
1047A ASN* 1.3 77.2 - - - +
1049A PHE* 1.4 60.9 + - - +
1051A LEU* 3.2 7.2 + - + +
1052A LEU* 3.1 50.0 + - + +
1066A VAL* 3.9 26.5 - - + -
1068A THR* 4.3 2.6 - - + +
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Residues in contact with PHE1049 (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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833A THR 3.6 17.9 - - - -
835A VAL* 3.9 27.1 - - + -
840A LEU* 4.9 1.1 - - + -
881A ALA 3.5 10.5 - - - +
884A LEU* 3.7 13.9 - - + -
885A ALA* 3.4 45.5 - - - +
888A SER* 4.2 0.9 - - - -
1045A PRO 3.1 13.2 + - - +
1046A ALA 3.3 7.2 - - - +
1048A TYR* 1.4 77.0 - - - +
1050A HIS* 1.3 80.1 + + - +
1052A LEU* 3.4 1.0 + - - -
1053A ARG* 3.0 51.1 + - + +
1085A PHE* 3.5 35.7 - + + -
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Residues in contact with HIS1050 (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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833A THR* 2.7 26.9 + - - +
834A ALA* 3.9 11.2 - - - -
1046A ALA* 2.9 30.6 + - + +
1047A ASN* 4.1 2.9 - - - +
1049A PHE* 1.3 90.5 - + - +
1051A LEU* 1.3 54.5 + - - +
1053A ARG* 3.8 2.3 - - - +
1054A ARG* 2.7 36.6 + - - +
1084A ASP 2.7 29.6 + - - -
1085A PHE* 3.9 5.4 - - - -
1088A SER* 3.1 26.7 + - - -
1089A LYS* 3.7 14.0 - - - -
1090A PHE* 3.4 24.0 - - - +
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Residues in contact with LEU1051 (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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1038A THR* 5.1 0.2 - - + -
1040A ALA* 3.8 27.1 - - + -
1042A PRO* 3.8 18.6 - - + -
1047A ASN 3.0 18.4 + - - +
1048A TYR* 3.2 9.8 + - + +
1050A HIS* 1.3 76.0 - - - +
1052A LEU* 1.4 57.5 + - + +
1054A ARG* 3.4 31.7 + - - +
1055A HIS* 3.0 28.3 + - - +
1064A LEU* 4.0 16.4 - - + -
1066A VAL* 4.0 22.7 - - + -
1090A PHE* 3.7 25.0 - - + -
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Residues in contact with LEU1052 (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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882A GLU* 4.0 14.1 - - + +
885A ALA* 4.0 21.3 - - + -
886A LEU* 4.5 9.4 - - + -
889A LEU* 4.3 2.7 - - + +
970A MET* 3.6 20.0 - - + +
972A LEU* 3.8 24.5 - - + -
1006A VAL* 4.6 11.9 - - + -
1048A TYR* 3.1 58.1 + - + +
1049A PHE 3.9 3.8 - - - +
1051A LEU* 1.4 72.2 - - + +
1053A ARG* 1.3 60.5 + - - +
1055A HIS* 3.4 5.9 + - - +
1056A GLY* 3.0 24.4 + - - -
1064A LEU* 4.7 6.5 - - + -
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Residues in contact with ARG1053 (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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832A ALA 4.6 1.0 + - - -
833A THR* 2.9 43.7 + - + -
834A ALA 4.0 3.2 + - - -
835A VAL* 3.5 15.3 - - - +
885A ALA* 3.8 12.3 - - + -
888A SER* 3.3 27.2 + - - -
889A LEU* 3.7 19.7 - - - +
892A GLU* 2.9 43.5 + - - -
1049A PHE* 3.0 39.3 + - + +
1050A HIS 3.8 0.4 - - - +
1052A LEU* 1.3 71.5 - - - +
1054A ARG* 1.4 67.4 + - - +
1056A GLY 3.4 1.0 + - - -
1057A LYS* 3.0 49.8 + - + +
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Residues in contact with ARG1054 (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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831A LEU* 6.1 3.1 - - + +
833A THR* 3.5 15.6 - - + +
1038A THR* 3.8 15.6 - - - +
1050A HIS 2.7 23.3 + - - +
1051A LEU* 3.4 30.9 + - - +
1053A ARG* 1.4 69.9 - - - +
1055A HIS* 1.3 63.1 + - - +
1057A LYS* 3.2 2.2 + - - -
1058A ASP* 3.0 42.9 + - + +
1090A PHE* 3.5 28.6 - - + -
1092A SER* 5.8 0.6 - - - -
1142A GLN* 2.9 29.7 + - - -
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Residues in contact with HIS1055 (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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970A MET* 4.1 10.1 - - + -
1004A ASP* 2.7 53.3 + - - +
1006A VAL* 3.4 23.0 - - + +
1038A THR* 5.6 2.4 + - - -
1051A LEU 3.0 18.4 + - - +
1052A LEU* 3.4 7.0 - - - +
1054A ARG* 1.3 76.7 - - - +
1056A GLY* 1.3 60.1 + - - +
1058A ASP* 3.0 30.5 + - - +
1062A ARG 3.1 28.4 + - - -
1064A LEU* 3.5 33.1 - - + +
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Residues in contact with GLY1056 (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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889A LEU* 4.7 2.9 - - - -
894A LYS* 2.9 35.0 + - - +
970A MET* 3.8 20.6 - - - -
1004A ASP* 4.6 5.0 - - - +
1052A LEU 3.0 13.7 + - - -
1053A ARG 3.4 1.3 + - - -
1055A HIS* 1.3 76.3 - - - +
1057A LYS* 1.4 61.5 + - - +
1059A GLY 5.2 1.8 + - - -
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Residues in contact with LYS1057 (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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831A LEU* 6.1 1.0 - - - -
832A ALA 3.8 18.8 - - - -
833A THR* 4.8 3.1 - - + -
889A LEU* 3.8 11.4 - - + -
892A GLU* 2.9 24.8 + - - +
894A LYS* 5.7 0.9 - - + -
1053A ARG* 3.0 55.0 + - + +
1054A ARG* 3.6 2.9 - - - +
1056A GLY* 1.4 79.4 - - - +
1058A ASP* 1.3 59.4 + - - +
1059A GLY 3.4 4.2 + - - -
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Residues in contact with ASP1058 (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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831A LEU* 6.5 0.9 - - - -
1004A ASP* 5.3 0.2 - - - +
1054A ARG* 3.0 30.8 + - + +
1055A HIS* 3.0 24.1 + - - +
1056A GLY 4.9 0.2 - - - -
1057A LYS* 1.3 76.3 - - - +
1059A GLY* 1.3 59.6 + - - +
1060A ILE* 3.0 57.3 + - + +
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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