Contacts of the helix formed by residues 101 - 108 (chain A) in PDB entry 2AXT
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 SER 101 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 6.4 0.2 - - - -
99A ALA* 3.1 9.7 - - - +
100A ALA* 1.3 83.5 - - - +
102A LEU* 1.3 66.5 + - - +
103A ASP* 3.6 14.0 + - - +
104A GLU* 2.9 26.2 + - - +
105A TRP 3.0 8.8 + - - -
1I MET* 5.6 8.1 - - - -
95O LYS* 5.2 8.2 - - - +
96O LEU 4.8 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 4.2 23.5 - - + +
101A SER* 1.3 71.8 - - - +
103A ASP* 1.3 53.0 + - - +
105A TRP* 2.6 39.2 + - + +
106A LEU* 2.6 40.9 + - + +
566A BCR 3.9 22.4 - - + -
487C UNK 4.7 13.0 - - + -
488C UNK 4.1 25.6 - - + -
489C UNK 3.7 31.0 - - + -
1I MET* 5.7 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SER* 3.2 11.9 + - - +
102A LEU* 1.3 74.5 + - - +
104A GLU* 1.3 56.7 + - - +
106A LEU* 3.3 9.3 + - - +
107A TYR* 2.9 31.9 + - - +
489C UNK 3.8 25.7 - - - +
95O LYS* 5.3 10.5 - - + +
97O VAL* 3.6 9.3 - - + +
135O GLN* 2.7 39.1 + - + +
141O ARG* 4.7 1.4 + - - -
5075b TRP 5.2 2.1 - - - +
5076b SER* 5.8 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 2.8 18.5 + - - +
98A GLU 3.9 2.8 - - - +
99A ALA* 3.4 11.2 - - + -
100A ALA* 3.1 31.4 + - - +
101A SER* 2.9 16.8 + - - +
103A ASP* 1.3 78.1 - - - +
105A TRP* 1.3 64.0 + - - +
107A TYR 3.3 0.2 + - - -
108A ASN* 2.6 39.1 + - - +
96O LEU 4.3 6.1 - - - +
97O VAL* 3.7 16.5 - - - +
98O THR 3.3 13.0 - - - +
99O ARG* 2.8 32.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 3.4 26.2 + + - -
95A PRO* 3.8 5.4 - - + -
96A ILE* 3.3 46.2 - - + +
99A ALA* 3.7 12.3 - - + -
101A SER 3.0 6.4 + - - +
102A LEU* 2.6 36.7 + - + +
104A GLU* 1.3 73.3 - - - +
106A LEU* 1.3 65.2 + - + -
108A ASN 3.9 0.7 - - - -
109A GLY 3.3 2.8 + - - -
110A GLY* 2.6 64.9 + - - -
111A PRO* 3.4 35.9 - - + -
114A LEU* 4.1 14.6 - - + -
566A BCR 3.4 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 5.1 2.5 - - + -
56A PRO* 3.9 36.7 - - + +
57A PRO 4.9 0.2 - - - -
58A VAL* 3.2 19.8 - - + +
102A LEU* 2.6 27.8 + - + +
103A ASP* 3.7 6.1 - - - +
105A TRP* 1.3 79.8 - - + +
107A TYR* 1.3 65.2 + - - +
108A ASN 3.1 1.6 - - - -
109A GLY* 3.1 10.6 + - - -
111A PRO* 3.8 27.4 - - + +
566A BCR 3.9 37.0 - - + -
489C UNK 4.4 21.8 - - + -
135O GLN* 6.0 0.4 - - - +
141O ARG* 4.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO 4.0 3.4 - - - -
58A VAL* 3.6 0.2 - - - -
59A ASP* 3.0 43.9 + - + +
64A ARG* 4.1 23.0 + - - +
66A PRO* 3.5 24.7 - - + +
103A ASP 2.9 17.3 + - - +
104A GLU 3.9 2.7 - - - +
106A LEU* 1.3 77.3 - - - +
108A ASN* 1.3 67.4 + - - +
109A GLY 3.6 0.2 + - - -
97O VAL* 3.4 42.6 - - + +
98O THR* 5.2 4.9 - - + -
133O THR* 3.9 24.8 + - + +
141O ARG* 3.1 46.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 3.7 4.0 - - - -
59A ASP* 5.3 2.1 - - - +
86A SER* 2.8 38.6 + - - -
88A ALA* 5.7 3.1 - - - +
89A ILE* 3.4 13.7 - - + +
94A TYR* 3.8 17.3 - - + -
104A GLU* 2.6 42.2 + - - +
107A TYR* 1.3 87.6 - - - +
109A GLY* 1.3 59.4 + - - +
110A GLY 3.5 0.4 - - - -
97O VAL 3.3 20.5 + - - +
98O THR* 5.1 4.2 - - - +
99O ARG* 4.3 17.6 + - - +
----------------------------------------------------------
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