Contacts of the helix formed by residues 81 - 89 (chain I) in PDB entry 6ALG
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 81 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I PHE* 1.3 77.2 - - - +
82I VAL* 1.3 67.3 - - + +
83I GLN* 4.7 3.3 - - - +
84I GLU* 3.3 32.3 - - - +
85I CYS* 3.2 20.6 + - - +
92I TYR* 4.2 4.5 - - - -
1032I LYS* 6.1 0.9 - - - -
1035I LYS* 4.6 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I ASP* 1.3 76.4 - - - +
83I GLN* 1.3 64.5 + - + +
85I CYS* 3.0 4.4 + - - +
86I GLN* 2.9 46.7 + - + +
92I TYR* 3.6 36.3 - - + +
131I THR* 4.0 33.2 - - + +
137I VAL* 4.9 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 83 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I ASP* 3.5 4.3 - - - +
82I VAL* 1.3 81.6 - - + +
84I GLU* 1.3 60.8 + - + +
85I CYS 3.2 0.3 + - - -
86I GLN* 3.3 10.6 + - - +
87I ILE* 3.0 40.2 + - + +
752I ASN* 5.3 6.9 + - - +
753I LEU 5.5 1.6 + - - -
754I THR* 3.9 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I PHE* 5.2 2.5 - - + -
81I ASP* 3.3 29.3 + - - +
82I VAL 3.4 0.4 - - - -
83I GLN* 1.3 79.1 - - + +
85I CYS* 1.3 56.5 + - - +
87I ILE* 3.9 18.3 - - - +
88I ARG* 2.9 58.3 + - - +
1032I LYS* 4.9 19.3 + - - -
1035I LYS* 6.2 4.0 - - + -
1036I ILE* 5.9 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 85 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I PHE* 4.0 15.9 - - + +
81I ASP 3.2 20.4 + - - +
82I VAL* 3.0 8.1 + - - +
84I GLU* 1.3 75.7 - - - +
86I GLN* 1.3 60.3 + - - +
87I ILE 3.3 0.2 - - - -
88I ARG* 4.4 3.6 - - - +
89I GLY* 3.0 23.2 + - - -
90I VAL* 3.2 39.9 + - - +
91I THR 3.2 23.3 - - - -
92I TYR* 3.6 14.4 - - + -
137I VAL* 4.5 3.6 - - + -
140I GLY* 4.2 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I VAL* 2.9 28.2 + - - +
83I GLN* 3.7 10.3 - - - +
85I CYS* 1.3 76.6 - - - +
87I ILE* 1.3 65.2 + - + +
89I GLY* 4.1 1.2 + - - -
131I THR* 6.0 0.6 - - - +
137I VAL* 4.1 22.8 - - + +
140I GLY* 3.6 31.9 - - - +
141I THR 4.9 0.2 - - - +
142I GLU* 3.5 33.0 + - - +
757I THR* 5.8 1.0 + - - +
758I ARG 5.6 1.7 - - - +
1051I LYS* 5.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 87 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I GLN* 3.0 24.5 + - + +
84I GLU* 3.9 20.0 - - - +
86I GLN* 1.3 81.2 - - + +
88I ARG* 1.3 63.0 + - + +
89I GLY* 4.8 0.2 - - - -
757I THR* 6.1 0.9 - - - +
932I GLN* 3.4 40.8 - - + +
934I PHE* 3.4 17.7 - - + -
1051I LYS* 4.3 9.7 + - - +
1053I TYR* 5.6 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I PHE* 3.5 52.9 - - - -
84I GLU* 2.9 53.6 + - - +
85I CYS* 4.4 1.3 - - - +
87I ILE* 1.3 80.5 - - + +
89I GLY* 1.3 56.4 + - - +
90I VAL* 3.7 14.8 - - + +
934I PHE* 3.9 26.5 - - + -
1035I LYS* 4.1 22.2 + - - +
1036I ILE* 5.7 0.8 - - - +
1038I GLN* 6.3 0.9 - - - -
1040I ASP* 3.8 31.5 + - + -
1041I ASP* 4.7 11.0 - - - +
1051I LYS* 5.1 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 89 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I CYS 3.0 9.9 + - - -
86I GLN 4.6 1.3 - - - -
87I ILE 3.6 1.2 - - - -
88I ARG* 1.3 78.1 - - - +
90I VAL* 1.3 65.5 + - - +
139I ASN* 3.3 14.2 - - - +
140I GLY* 3.1 29.1 + - - -
1051I LYS* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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