Contacts of the helix formed by residues 970 - 976 (chain B) in PDB entry 3U44
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 ASP 970 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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967B LYS* 3.4 18.8 - - + +
968B GLY 4.3 0.2 + - - -
969B LEU* 1.3 75.2 - - - +
971B LEU* 1.3 65.6 + - - +
972B ALA* 2.7 30.5 + - - +
973B GLU* 2.9 39.9 + - + +
974B VAL* 3.2 12.8 + - - +
1115B MET* 5.4 1.4 - - - +
1147B GLU 4.9 3.8 - - - +
1149B ASP* 4.8 5.4 - - - +
41X A 5.6 2.5 + - - -
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Residues in contact with LEU 971 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969B LEU* 4.1 14.9 + - + +
970B ASP* 1.3 73.1 + - - +
972B ALA* 1.3 63.5 + - - +
974B VAL* 3.0 19.5 + - + +
975B TYR* 3.1 13.5 + - - +
1040B LEU* 4.2 22.4 - - + -
1080B VAL* 5.8 4.0 - - + -
1088B LEU* 3.6 34.1 - - + +
1149B ASP* 3.5 54.4 + - + +
1152B ILE* 4.0 11.5 - - + +
1153B LEU* 4.0 20.0 - - + -
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Residues in contact with ALA 972 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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970B ASP* 2.7 25.4 + - - +
971B LEU* 1.3 74.0 - - - +
973B GLU* 1.3 59.4 + - - +
974B VAL 3.4 0.2 + - - -
975B TYR* 3.4 5.9 + - - +
976B TYR* 3.3 24.6 - - - -
1115B MET* 3.4 20.6 - - + -
1145B LYS 4.6 0.2 - - - +
1146B ALA* 5.1 0.7 - - - -
1147B GLU* 4.2 24.7 + - + +
1149B ASP* 5.9 0.4 - - - +
1152B ILE* 3.3 19.2 - - + +
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Residues in contact with GLU 973 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967B LYS* 5.8 3.8 + - - -
970B ASP* 2.9 31.5 + - + +
972B ALA* 1.3 79.0 - - - +
974B VAL* 1.3 60.9 + - - +
976B TYR* 3.4 3.4 + - - +
977B GLY 3.4 3.1 + - - -
978B LEU* 3.0 51.2 + - + +
979B ALA* 3.9 20.8 + - + +
1115B MET* 4.4 13.5 - - - -
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Residues in contact with VAL 974 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969B LEU* 3.4 24.2 - - + -
970B ASP 3.4 15.3 - - - +
971B LEU* 3.0 16.5 + - + +
973B GLU* 1.3 76.2 - - - +
975B TYR* 1.3 66.2 + - - +
977B GLY* 2.9 13.9 + - - -
979B ALA* 3.4 26.5 - - + +
980B LEU* 3.7 10.5 - - + +
983B LEU* 3.4 28.9 - - + -
1088B LEU* 4.8 8.7 - - + -
1091B HIS* 3.7 12.4 + - + -
1092B VAL* 4.5 4.5 - - + -
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Residues in contact with TYR 975 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971B LEU 3.1 5.7 + - - -
972B ALA 3.7 2.0 - - - +
973B GLU 3.3 0.2 - - - -
974B VAL* 1.3 77.1 - - - +
976B TYR* 1.3 93.0 + + - +
977B GLY 3.2 0.7 + - - -
1091B HIS* 2.8 36.9 + + - -
1095B THR* 4.6 2.6 + - - -
1152B ILE* 3.4 37.7 - - + -
1155B TRP* 4.3 30.0 + + + +
1156B ILE* 3.3 30.5 - - + -
1159B GLU* 5.3 5.0 + - - -
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Residues in contact with TYR 976 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799B ASN* 3.5 27.4 + - - +
972B ALA 3.3 24.7 - - - -
973B GLU* 3.4 5.5 + - - +
974B VAL 3.2 0.2 - - - -
975B TYR* 1.3 103.8 - + - +
977B GLY* 1.3 62.0 + - - +
978B LEU* 3.3 8.4 + - + +
1095B THR* 5.4 1.1 - - - -
1115B MET* 3.8 9.4 - - + -
1143B PRO 4.9 1.0 + - - -
1144B LEU* 3.4 56.7 - - + -
1145B LYS* 3.7 18.2 + - - +
1152B ILE* 4.6 5.2 - - + -
1155B TRP* 4.2 17.7 - - - -
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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