Contacts of the helix formed by residues 982 - 992 (chain D) in PDB entry 6AH0
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 THR 982 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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968D ASN 5.3 3.6 - - - -
969D LEU 3.4 15.9 + - - -
970D VAL* 4.8 0.4 - - - +
980D GLN 3.8 0.6 + - - -
981D VAL* 1.3 74.8 - - - +
983D GLU* 1.3 57.7 - - - +
984D LEU 3.0 3.8 - - - +
985D GLY* 2.7 21.8 + - - +
986D ARG* 3.0 9.9 + - - -
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Residues in contact with GLU 983 (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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982D THR* 1.3 71.0 - - - +
984D LEU* 1.3 56.7 + - - +
986D ARG* 3.3 3.1 + - - +
987D ILE* 2.9 26.3 + - - -
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Residues in contact with LEU 984 (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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968D ASN 5.0 5.8 + - - -
969D LEU* 5.1 2.2 - - - -
982D THR* 3.0 1.4 - - - +
983D GLU* 1.3 75.2 - - - +
985D GLY* 1.3 57.4 + - - +
987D ILE* 3.3 2.2 + - - +
988D ALA* 2.9 25.5 + - - -
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Residues in contact with GLY 985 (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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902D ASN 6.0 1.7 - - - -
906D VAL* 6.2 1.6 - - - -
968D ASN 4.7 0.2 + - - -
969D LEU* 3.7 29.7 + - - +
981D VAL* 6.1 0.2 - - - -
982D THR 2.7 11.0 + - - -
984D LEU* 1.3 72.7 - - - +
986D ARG* 1.3 59.2 + - - -
988D ALA* 3.1 2.8 + - - -
989D SER* 2.9 26.2 + - - -
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Residues in contact with ARG 986 (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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906D VAL* 5.7 8.7 - - - +
982D THR 3.0 11.2 + - - -
983D GLU* 3.3 4.2 + - - +
985D GLY* 1.3 74.1 - - - +
987D ILE* 1.3 63.4 + - - +
989D SER* 3.3 2.2 + - - +
990D HIS* 2.9 22.5 + - - -
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Residues in contact with ILE 987 (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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983D GLU 2.9 15.3 + - - -
984D LEU* 3.8 3.1 - - - +
986D ARG* 1.3 74.5 - - - +
988D ALA* 1.3 62.1 + - - +
990D HIS* 3.8 1.0 - - - +
991D TYR* 3.0 21.3 + - - -
1094D ALA* 5.3 11.7 - - - +
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Residues in contact with ALA 988 (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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984D LEU 2.9 14.8 + - - -
985D GLY* 3.1 4.0 + - - -
987D ILE* 1.3 77.7 - - - +
989D SER* 1.3 61.2 + - - +
992D TYR* 3.1 18.7 + - - -
993D ILE* 3.2 25.5 + - - +
998D VAL* 6.5 1.1 - - - +
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Residues in contact with SER 989 (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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595D ILE* 5.5 5.7 - - - -
598D ARG* 5.6 6.0 - - - -
903D ALA* 5.0 17.9 - - - +
985D GLY 2.9 14.0 + - - -
986D ARG* 3.8 2.5 - - - +
988D ALA* 1.3 76.2 - - - +
990D HIS* 1.3 61.3 + - - +
992D TYR* 3.1 14.7 + - - +
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Residues in contact with HIS 990 (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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595D ILE* 5.2 10.6 - - - +
598D ARG 5.3 12.3 + - - -
599D LYS* 5.4 4.7 - - - +
986D ARG 2.9 16.1 + - - -
987D ILE* 3.8 1.6 - - - +
989D SER* 1.3 75.0 - - - +
991D TYR* 1.3 57.5 + - - +
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Residues in contact with TYR 991 (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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987D ILE 3.0 16.0 + - - -
988D ALA 4.0 0.2 - - - -
990D HIS* 1.3 77.4 - - - +
992D TYR* 1.3 65.0 + - - +
993D ILE* 3.1 5.2 + - - -
1090D ARG* 4.6 25.0 - - - +
1094D ALA* 6.1 2.5 - - - +
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Residues in contact with TYR 992 (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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988D ALA 3.1 7.3 + - - -
989D SER* 3.1 10.8 + - - +
990D HIS 3.5 0.6 - - - -
991D TYR* 1.3 78.0 - - - +
993D ILE* 1.3 60.9 + - - +
994D THR 4.0 1.0 + - - -
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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