Contacts of the helix formed by residues 96 - 107 (chain A) in PDB entry 3GA1
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 96 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLN* 4.4 12.5 - - - +
77A SER* 5.5 0.2 - - - +
93A ASN* 2.8 31.0 + - - +
94A VAL 5.1 1.4 - - - +
95A GLY* 1.3 83.2 - - - +
97A GLN* 1.3 66.1 + - - +
98A ASP* 3.2 8.9 - - - +
99A LEU* 3.2 24.0 + - + +
100A LEU* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A MET* 6.2 1.3 - - - -
93A ASN* 3.3 13.4 + - - +
96A ASP* 1.3 78.2 - - - +
98A ASP* 1.3 63.5 + - - +
100A LEU* 3.6 10.4 - - - +
101A MET* 2.9 42.5 + - + +
126A NO3 2.9 28.2 + - - +
6B GLN* 2.8 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY 4.1 5.9 - - - +
96A ASP* 3.8 14.2 - - - +
97A GLN* 1.3 80.0 - - - +
99A LEU* 1.3 73.3 + - - +
101A MET* 3.8 4.9 - - - +
102A TYR* 2.9 30.7 + - - +
126A NO3 4.4 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA 4.3 9.6 - - - +
74A GLN* 3.6 33.9 - - + +
76A GLN* 6.6 0.2 - - + -
77A SER* 3.4 20.2 - - - +
96A ASP* 3.5 26.0 - - + +
98A ASP* 1.3 83.9 + - - +
100A LEU* 1.3 66.4 + - - +
102A TYR* 3.3 11.8 + - + +
103A THR* 2.9 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A SER* 3.8 25.5 + - - +
80A GLN* 3.7 33.9 - - + +
81A ILE* 3.8 24.5 - - + -
90A LEU* 4.3 7.4 - - + -
91A SER 3.9 1.6 - - - +
93A ASN* 4.1 10.3 - - + +
96A ASP 2.9 16.3 + - - +
97A GLN* 3.6 11.0 - - - +
99A LEU* 1.3 76.6 - - - +
101A MET* 1.3 68.9 + - + +
103A THR* 3.3 1.4 + - - -
104A ALA* 2.9 28.1 + - - +
6B GLN* 3.5 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 4.1 15.0 - - + -
97A GLN* 2.9 37.1 + - + +
98A ASP* 3.8 5.2 - - - +
100A LEU* 1.3 93.4 - - + +
102A TYR* 1.3 64.4 + - - +
104A ALA* 3.2 4.7 + - + +
105A GLY* 2.9 21.1 + - - -
112A ILE* 4.6 9.6 - - + -
113A MET* 3.5 33.7 - - + +
6B GLN* 3.9 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 4.2 27.4 - - + -
98A ASP 2.9 17.1 + - - +
99A LEU* 3.6 12.6 - - + +
101A MET* 1.3 77.5 - - - +
103A THR* 1.3 55.2 + - - +
105A GLY* 3.3 2.2 + - - -
106A PHE* 2.7 47.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 5.0 1.3 + - - -
73A VAL* 3.7 41.2 - - + +
74A GLN 4.6 0.2 + - - -
77A SER* 4.0 18.5 + - - -
78A PHE* 4.9 1.8 - - - +
81A ILE* 4.6 8.7 - - + -
99A LEU* 2.9 25.2 + - - +
100A LEU 3.7 3.6 - - - -
102A TYR* 1.3 75.8 - - - +
104A ALA* 1.3 60.7 + - - +
106A PHE* 3.6 5.5 - - - +
107A LEU* 2.8 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 3.7 18.5 - - + +
100A LEU 2.9 18.0 + - - +
101A MET* 3.7 9.0 - - + +
103A THR* 1.3 76.5 - - - +
105A GLY* 1.3 62.1 + - - +
108A GLN 3.1 4.3 + - - -
109A ILE* 3.1 40.3 + - + +
112A ILE* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A MET 2.9 13.8 + - - -
102A TYR* 3.7 2.9 - - - -
104A ALA* 1.3 73.3 - - - +
106A PHE* 1.3 66.5 + - - +
108A GLN* 2.8 21.0 + - - +
109A ILE 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 3.6 43.0 - + - -
70A PRO* 3.5 34.5 - - + -
72A ALA* 4.5 15.3 - - + -
73A VAL* 4.2 12.6 - - + -
102A TYR* 2.7 34.4 + + + +
103A THR* 3.3 8.0 + - - +
105A GLY* 1.3 73.3 - - - +
107A LEU* 1.3 71.6 + - + +
108A GLN* 3.1 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER* 2.6 30.6 + - - +
54A TYR* 3.3 27.6 - - + +
55A PHE* 4.3 11.4 - - + -
69A LEU* 4.2 16.6 - - + -
73A VAL* 4.8 0.9 - - + -
78A PHE* 3.8 33.9 - - + -
81A ILE* 4.2 13.9 - - + -
103A THR* 2.8 36.3 + - + +
106A PHE* 1.3 87.6 - - + +
108A GLN* 1.3 66.6 + - - +
109A ILE* 3.2 13.0 + - + -
----------------------------------------------------------
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