Contacts of the helix formed by residues 966 - 970 (chain A) in PDB entry 1DJL
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 ASN 966 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965A ALA* 1.3 75.6 - - - +
967A ASP* 1.3 67.9 + - - +
968A THR* 3.2 0.9 + - - -
969A VAL* 3.0 14.9 + - - +
970A ASN* 3.2 12.6 + - - +
999A LYS* 3.7 5.8 - - - +
1003A GLY 3.1 21.2 + - - -
1004A VAL* 3.5 2.0 - - - +
1005A GLY 3.4 12.7 - - - +
1009A VAL 4.8 3.4 + - - +
1011A ASN* 3.1 37.1 + - - +
1014A PHE* 3.7 10.1 - - - -
1136A NAP 2.9 47.1 + - + +
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Residues in contact with ASP 967 (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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966A ASN* 1.3 76.0 - - - +
968A THR* 1.3 60.9 + - - +
969A VAL 3.2 1.6 + - - -
970A ASN* 3.4 17.9 + - - +
981A ILE* 5.6 1.1 - - + -
986A VAL* 3.8 1.0 - - - +
1005A GLY* 3.7 13.9 + - - -
1006A TYR 3.2 6.1 + - - -
1007A ALA* 2.6 40.7 + - + +
1009A VAL* 4.7 10.2 - - - +
1136A NAP 2.7 51.9 + - - +
1137A GOL 3.1 29.3 + - - -
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Residues in contact with THR 968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A PRO 5.0 1.0 + - - -
920A HIS* 3.3 49.8 - - + +
922A VAL* 4.2 4.9 - - + +
923A ALA* 3.9 14.9 - - - +
965A ALA* 3.7 14.2 - - - +
967A ASP* 1.3 74.4 - - - +
969A VAL* 1.3 62.0 + - - +
970A ASN 3.6 0.7 - - - -
986A VAL* 3.5 4.8 - - - +
987A LEU* 2.8 29.7 + - - +
1136A NAP 2.7 36.3 + - - +
1137A GOL 4.8 1.6 - - - +
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Residues in contact with VAL 969 (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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887A THR* 3.9 15.0 - - - +
962A VAL* 4.0 17.3 - - + -
965A ALA* 4.1 4.5 - - + +
966A ASN* 3.0 17.2 + - - +
968A THR* 1.3 88.4 + - - +
970A ASN* 1.3 61.0 + - - +
971A SER 3.5 3.3 + - - -
986A VAL* 4.4 0.4 - - - -
987A LEU* 3.7 20.4 - - + +
989A VAL* 3.8 32.3 - - + -
990A TRP* 4.0 5.1 - - - -
1011A ASN* 3.5 6.9 + - - +
1013A ILE* 3.6 31.2 - - + +
1014A PHE* 6.2 0.4 - - + -
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Residues in contact with ASN 970 (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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966A ASN* 3.5 9.3 + - - +
967A ASP* 3.4 20.0 + - - +
968A THR 3.6 0.8 - - - -
969A VAL* 1.3 73.8 - - - +
971A SER* 1.3 64.1 + - - +
972A ALA* 2.8 38.0 + - - +
973A ALA* 3.1 20.8 + - - +
981A ILE* 3.7 13.7 - - + +
986A VAL* 3.8 6.2 - - - +
990A TRP* 4.3 1.8 - - - -
1009A VAL* 3.7 20.4 + - - +
1010A ASP 3.1 21.6 + - - -
1011A ASN* 3.5 21.2 - - - +
1012A PRO* 3.3 4.9 - - - +
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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