Contacts of the helix formed by residues 1048 - 1056 (chain A) in PDB entry 4XHT
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 THR1048 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017A ILE* 6.0 0.5 - - - +
1047A LEU* 1.3 88.5 + - + +
1049A GLU* 1.3 59.3 + - - +
1050A GLU* 3.5 8.1 + - - +
1051A ASN* 3.0 32.7 + - - +
1052A GLU* 2.9 34.6 + - - +
1017C ILE* 4.3 22.7 - - + -
1048C THR* 4.8 18.6 - - + +
1051C ASN* 5.9 3.6 - - - +
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Residues in contact with GLU1049 (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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1048A THR* 1.3 74.0 - - - +
1050A GLU* 1.3 62.5 + - - +
1052A GLU* 3.4 10.1 + - - +
1053A GLU* 3.0 23.9 + - - +
1076B GLN 5.0 0.3 - - - +
1077B GLU* 5.7 0.3 - - - +
1081B ARG* 4.1 22.7 + - - +
1017C ILE* 6.0 0.8 - - - +
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Residues in contact with GLU1050 (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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1014A GLY 4.1 12.3 - - - +
1015A PHE* 5.7 1.2 - - + -
1017A ILE* 3.9 22.8 + - + +
1018A PRO* 3.7 29.6 - - + +
1048A THR* 3.2 8.7 + - - +
1049A GLU* 1.3 79.6 - - - +
1051A ASN* 1.3 62.6 + - - +
1053A GLU* 3.4 15.3 + - - +
1054A ALA* 3.1 20.4 + - - +
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Residues in contact with ASN1051 (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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1017A ILE* 4.3 9.8 + - - +
1018A PRO* 3.6 22.5 - - - +
1021A TRP* 3.5 45.8 - - + +
1046A PRO* 3.6 17.7 - - + -
1047A LEU* 4.4 6.8 - - - +
1048A THR* 3.0 24.2 + - - +
1050A GLU* 1.3 74.3 - - - +
1052A GLU* 1.3 66.3 + - - +
1054A ALA* 3.3 7.6 + - - +
1055A MET* 3.0 26.9 + - - +
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Residues in contact with GLU1052 (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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1046A PRO* 3.5 10.2 - - + +
1047A LEU 5.9 0.3 - - - -
1048A THR 2.9 17.6 + - - +
1049A GLU* 3.5 14.1 + - - +
1051A ASN* 1.3 77.2 - - - +
1053A GLU* 1.3 63.4 + - - +
1055A MET* 3.1 12.0 + - - +
1056A GLU* 3.1 19.1 + - - +
1043B PRO* 4.9 2.4 - - - +
1076B GLN 4.0 6.1 - - - +
1077B GLU* 3.6 3.1 - - + -
1078B THR* 2.8 38.6 + - - +
1079B PHE* 3.1 32.5 + - + -
1081B ARG* 2.9 38.5 + - - -
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Residues in contact with GLU1053 (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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1015A PHE* 4.1 19.6 - - + -
1049A GLU 3.0 13.4 + - - +
1050A GLU* 3.5 16.8 - - - +
1052A GLU* 1.3 75.3 - - - +
1054A ALA* 1.3 62.3 + - - +
1056A GLU* 3.2 4.3 + - - +
1057A ASN* 3.2 21.2 + - + +
1075B GLY 4.9 2.6 - - - +
1076B GLN* 3.4 47.0 + - - +
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Residues in contact with ALA1054 (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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1015A PHE* 4.1 16.8 - - + -
1018A PRO* 3.5 37.7 - - + -
1021A TRP* 5.6 0.4 - - + -
1050A GLU 3.1 6.6 + - - +
1051A ASN 3.6 7.2 - - - +
1053A GLU* 1.3 77.2 - - - +
1055A MET* 1.3 62.2 + - - +
1057A ASN* 3.0 12.4 + - - +
1060A PHE* 3.2 39.7 - - + +
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Residues in contact with MET1055 (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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1021A TRP* 3.8 33.2 - - + -
1044A LEU* 4.7 11.0 - - + +
1046A PRO* 4.1 14.1 - - + -
1051A ASN 3.0 17.2 + - - +
1052A GLU 3.1 8.2 + - - +
1054A ALA* 1.3 76.0 - - - +
1056A GLU* 1.3 62.7 + - - +
1057A ASN 3.4 0.2 - - - -
1060A PHE* 3.9 16.6 - - - -
1061A GLN* 2.8 24.5 + - - +
1064A LEU* 3.5 19.3 - - + -
1080A TRP* 3.3 45.1 + - + +
1078B THR* 4.3 11.2 - - - +
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Residues in contact with GLU1056 (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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1052A GLU 3.1 15.8 + - - +
1053A GLU 3.2 4.9 + - - +
1054A ALA 3.1 0.8 - - - -
1055A MET* 1.3 83.9 - - - +
1057A ASN* 1.3 60.6 + - - +
1058A GLU 3.8 1.6 + - - -
1061A GLN* 3.8 11.7 + - - +
1075B GLY* 3.7 39.5 + - - +
1076B GLN 4.0 1.6 - - - +
1077B GLU 3.5 31.2 - - - +
1078B THR* 2.9 27.9 + - - +
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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