Contacts of the helix formed by residues 944 - 954 (chain D) in PDB entry 3O33
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 944 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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924D PHE* 3.5 14.4 - - - +
925D GLN 3.3 3.5 - - - +
926D ASP 3.7 13.7 - - - +
927D PRO* 3.4 25.7 - - + +
928D VAL 5.6 0.2 - - - +
943D MET* 1.3 81.9 - - - +
945D LEU* 1.3 62.4 + - - +
946D SER* 2.5 37.3 + - - -
947D THR* 2.5 33.2 + - - -
948D ILE* 3.3 15.6 + - - +
972D ILE* 3.6 10.5 - - - -
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Residues in contact with LEU 945 (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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912D LEU* 3.9 9.2 - - + +
915D LEU* 3.9 35.7 - - + -
916D TYR* 3.5 28.0 + - + +
921D SER* 4.1 18.2 - - - -
924D PHE* 3.0 23.9 + - + +
925D GLN* 4.0 23.8 - - + +
944D ASP* 1.3 72.1 - - - +
946D SER* 1.3 57.2 + - - +
948D ILE* 3.3 3.8 + - + +
949D LYS* 2.8 29.6 + - - +
969D PHE* 3.9 13.7 - - + -
972D ILE* 3.9 17.3 - - + -
993D LEU* 5.3 2.9 - - + -
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Residues in contact with SER 946 (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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916D TYR* 3.2 12.3 + - - -
925D GLN 3.0 16.8 + - - -
926D ASP* 4.0 10.1 - - - -
927D PRO* 3.7 12.0 - - - +
944D ASP* 2.5 20.4 + - - -
945D LEU* 1.3 76.3 - - - +
947D THR* 1.3 58.7 + - - +
949D LYS* 3.4 6.6 + - - +
950D LYS* 2.9 29.1 + - - +
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Residues in contact with THR 947 (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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927D PRO* 4.7 3.5 - - - +
943D MET* 3.8 19.2 - - + -
944D ASP* 2.5 33.0 + - - -
945D LEU 3.2 0.4 - - - -
946D SER* 1.3 79.4 + - - +
948D ILE* 1.3 61.9 + - - +
950D LYS* 3.3 5.5 + - - +
951D ARG* 2.9 55.4 + - - +
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Residues in contact with ILE 948 (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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908D CYS* 4.2 9.0 - - - -
912D LEU* 3.8 15.7 - - + -
943D MET* 3.9 5.6 - - - -
944D ASP 3.5 7.9 - - - +
945D LEU* 3.3 8.6 + - + +
947D THR* 1.3 76.3 - - - +
949D LYS* 1.3 64.0 + - - +
951D ARG* 3.2 1.9 + - - +
952D LEU* 2.9 23.6 + - - +
959D TYR* 3.6 23.3 - - + +
965D PHE* 4.8 1.6 - - + -
968D ASP* 3.8 19.5 - - + +
969D PHE* 3.7 58.8 - - + +
972D ILE* 3.8 15.9 - - + -
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Residues in contact with LYS 949 (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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851D SER 2.7 29.7 + - - -
852D CYS 4.2 3.2 + - - -
853D HIS 3.1 16.2 + - - -
854D VAL* 4.2 17.4 - - + +
855D PRO* 4.9 1.1 - - + -
856D THR* 2.7 29.2 + - - +
912D LEU* 3.6 22.4 - - + +
916D TYR* 4.0 17.8 + - + +
945D LEU 2.8 17.9 + - - +
946D SER* 3.5 7.9 - - - +
948D ILE* 1.3 77.2 - - - +
950D LYS* 1.3 60.8 + - - +
952D LEU* 3.5 3.1 + - - +
953D GLN* 3.3 22.1 + - + +
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Residues in contact with LYS 950 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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946D SER 2.9 16.9 + - - +
947D THR* 3.9 5.4 - - - +
949D LYS* 1.3 75.8 - - - +
951D ARG* 1.3 66.7 + - - +
953D GLN* 3.2 17.7 + - - +
954D GLU* 3.1 40.7 + - + +
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Residues in contact with ARG 951 (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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943D MET* 3.6 19.7 - - - +
947D THR* 2.9 40.0 + - - +
948D ILE 3.2 0.6 + - - +
950D LYS* 1.3 78.3 - - - +
952D LEU* 1.3 56.0 + - - +
953D GLN 3.6 0.2 + - - -
954D GLU* 3.7 18.1 + - - +
957D SER* 2.7 34.7 + - - -
958D MET* 3.4 51.0 - - + +
959D TYR* 3.7 19.1 + - + +
968D ASP* 3.2 29.4 + - - -
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Residues in contact with LEU 952 (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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854D VAL* 5.2 0.9 - - + -
900D LEU* 3.6 31.0 - - + -
905D LYS* 3.6 33.1 - - + +
908D CYS* 3.7 33.9 - - + -
909D GLU* 3.5 32.5 - - + +
912D LEU* 4.0 11.7 - - + -
948D ILE 2.9 16.8 + - - +
949D LYS 3.8 4.9 - - - +
951D ARG* 1.3 77.9 - - - +
953D GLN* 1.3 61.4 + - - +
954D GLU 3.6 5.4 + - - +
957D SER* 4.3 5.2 - - - +
959D TYR* 3.9 11.6 - - + -
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Residues in contact with GLN 953 (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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855D PRO* 5.9 8.1 - - + -
856D THR* 6.4 0.4 - - - +
905D LYS* 4.9 7.6 - - - +
949D LYS* 3.3 15.1 + - + +
950D LYS* 3.2 25.7 + - - +
952D LEU* 1.3 79.5 - - - +
954D GLU* 1.3 69.8 + - - +
955D ASP* 3.4 7.8 + - - +
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Residues in contact with GLU 954 (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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950D LYS* 3.1 39.2 + - + +
951D ARG* 3.9 29.0 - - - +
952D LEU 3.4 3.2 - - - +
953D GLN* 1.3 84.0 - - - +
955D ASP* 1.3 68.3 + - - +
956D TYR 3.0 15.9 + - - +
957D SER* 3.2 19.0 + - - +
958D MET* 4.6 9.0 - - - +
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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