Contacts of the strand formed by residues 95 - 101 (chain C) in PDB entry 2AG1
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 VAL 95 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ALA* 3.7 24.0 - - + +
58C GLU* 3.9 29.6 - - + +
61C ALA* 4.6 0.2 - - + -
67C LEU* 4.4 1.8 - - - -
68C GLY 3.2 10.8 - - - +
70C ALA 4.2 1.1 - - - +
88C ALA* 4.5 2.0 - - + -
93C THR* 3.3 24.0 + - - +
94C PRO* 1.3 79.7 - - - +
96C LEU* 1.3 71.3 + - - +
97C PHE* 3.6 29.9 + - + -
149C ALA* 4.6 2.2 - - - -
155C GLY 3.8 2.8 + - - +
156C PRO* 3.3 3.1 - - + +
157C VAL* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 3.9 24.7 - - + -
67C LEU* 3.9 9.6 - - + +
68C GLY 2.9 12.5 + - - +
69C VAL* 3.5 11.5 - - + +
70C ALA 2.8 29.1 + - - +
95C VAL* 1.3 73.2 - - - +
97C PHE* 1.3 67.3 + - - +
98C LEU* 3.6 36.3 + - + -
142C VAL* 4.5 5.2 - - + +
145C ALA* 4.2 22.9 - - + -
146C ILE* 4.0 23.8 - - + +
149C ALA* 5.2 1.8 - - + -
157C VAL* 3.8 9.0 - - + +
159C LEU* 4.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLY* 4.0 9.9 - - - -
58C GLU* 5.1 0.2 - - + -
70C ALA* 3.6 24.2 - - + -
72C VAL* 6.0 3.8 - - + -
81C ALA* 4.3 12.6 - - + -
84C PRO* 3.7 22.4 - - + -
85C ILE* 3.6 44.9 - - + -
88C ALA* 4.5 1.6 - - + -
95C VAL* 3.6 30.7 - - + -
96C LEU* 1.3 74.2 - - - +
98C LEU* 1.3 61.3 + - - +
156C PRO* 3.8 17.9 - - + -
157C VAL 2.8 20.5 + - - +
158C LEU* 3.4 19.0 - - + +
159C LEU* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 4.0 25.4 - - + -
14C LEU* 4.2 8.5 - - + -
22C LEU* 4.7 7.9 - - + -
33C ILE* 4.8 3.1 - - + -
69C VAL* 3.8 22.7 - - + -
70C ALA 2.7 15.2 + - - +
71C LEU* 3.3 15.4 - - + +
72C VAL* 2.8 29.0 + - - +
96C LEU* 3.6 34.5 - - + -
97C PHE* 1.3 72.2 - - - +
99C THR* 1.3 59.0 + - - +
142C VAL* 4.9 2.0 - - + -
159C LEU* 3.6 20.6 - - + -
161C LEU* 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ILE* 4.5 2.2 - - - -
72C VAL* 3.2 23.6 - - - +
73C THR 3.5 7.1 + - - -
78C PHE* 3.5 12.8 - - + +
98C LEU* 1.3 75.1 - - - +
100C GLY* 1.3 70.0 + - - +
118C GLN* 3.8 10.1 - - - +
158C LEU* 3.8 24.9 - - + -
159C LEU 3.0 10.8 + - - +
160C ASP* 3.6 21.5 - - + +
161C LEU* 2.8 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C HIS* 4.7 3.8 - - - -
30C ILE* 3.6 20.4 - - - +
72C VAL 2.8 15.3 + - - -
74C ALA* 3.3 17.5 - - - -
99C THR* 1.3 87.4 + - - +
101C SER* 1.3 59.8 + - - -
118C GLN* 3.0 12.0 - - - +
161C LEU 3.5 9.2 - - - -
166C LEU* 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C HIS* 3.8 2.3 + - - -
74C ALA* 3.4 14.9 - - - +
100C GLY* 1.3 73.4 - - - -
102C GLY* 1.3 65.6 + - - +
118C GLN* 3.5 9.6 - - - +
131C ARG* 2.9 23.5 + - - -
160C ASP* 2.7 35.5 + - - -
161C LEU 3.5 3.8 + - - -
162C PRO* 3.5 6.4 - - - +
163C TRP* 3.0 22.3 + - - +
----------------------------------------------------------
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