Contacts of the strand formed by residues 128 - 138 (chain X) in PDB entry 2AT8
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 LYS 128 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123X LEU* 6.4 0.7 - - - -
124X HIS* 3.3 6.1 + - - +
125X LYS* 2.9 49.6 + - + +
126X GLY 3.7 1.6 - - - +
127X ASN* 1.3 80.1 - - - +
129X ASP* 1.3 66.4 + - - +
130X LEU* 4.8 15.0 - - - +
185X FDD 3.2 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 129 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1X ALA* 2.8 47.5 + - - -
2X CYS* 3.7 10.8 + - - -
32X GLU* 4.8 0.7 - - - +
35X ASP* 4.2 5.2 - - - +
122X CYS* 4.8 0.2 - - - -
123X LEU* 2.9 18.6 - - - +
124X HIS* 4.1 17.3 - - - +
125X LYS 4.9 0.2 - - - +
127X ASN 4.1 2.1 + - - +
128X LYS* 1.3 83.8 - - - +
130X LEU* 1.3 61.6 + - - +
131X GLY 2.9 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30X ASP* 2.6 29.6 - - - +
35X ASP* 3.1 35.8 - - + +
36X VAL* 3.7 11.2 - - + -
123X LEU* 3.0 28.7 + - + -
128X LYS* 4.8 13.0 - - - +
129X ASP* 1.3 76.0 - - - +
131X GLY* 1.3 58.7 + - - +
133X LEU* 4.9 2.8 - - + +
185X FDD 3.6 56.8 - - + +
186X NO 3.6 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 131 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1X ALA 3.6 12.1 - - - -
2X CYS* 3.5 14.7 - - - -
30X ASP* 3.7 7.0 - - - -
32X GLU* 3.7 4.3 - - - -
35X ASP* 3.4 7.0 + - - -
121X THR 3.5 6.4 - - - +
122X CYS* 4.0 3.1 - - - -
123X LEU 4.5 0.7 + - - -
129X ASP* 2.9 17.5 + - - -
130X LEU* 1.3 82.2 - - - +
132X ASP* 1.3 65.8 + - - -
133X LEU* 3.2 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1X ALA 4.1 1.6 + - - +
2X CYS* 3.5 7.1 - - - +
3X THR* 2.8 38.0 + - - +
4X LYS* 3.0 26.7 + - - +
29X LEU 3.6 1.7 - - - +
30X ASP* 3.2 4.4 + - - +
31X LEU* 2.9 51.2 + - + +
32X GLU* 5.1 0.4 - - - +
120X HIS* 2.8 33.6 + - + +
121X THR 3.9 0.7 - - - -
131X GLY* 1.3 68.8 - - - -
133X LEU* 1.3 58.4 + - - +
134X TYR* 4.1 3.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28X TYR* 4.4 17.5 - - + -
29X LEU 3.5 15.9 - - - +
30X ASP* 3.9 23.8 - - + +
36X VAL* 4.7 5.6 - - + -
119X ILE* 4.4 0.3 - - - +
120X HIS* 3.4 3.9 - - - -
121X THR* 2.8 52.0 + - + +
130X LEU* 4.9 2.2 - - + +
131X GLY 3.2 3.5 + - - +
132X ASP* 1.3 73.3 - - - +
134X TYR* 1.3 68.3 + - - +
135X ALA* 4.2 2.1 + - + -
185X FDD 3.5 31.0 - - + +
186X NO 3.5 31.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 134 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4X LYS* 3.4 29.3 - - - +
6X ALA* 5.1 3.2 - - + +
28X TYR* 3.2 6.9 - - - +
29X LEU* 2.8 43.0 + - + +
31X LEU* 4.0 30.1 - - + +
110X MET* 3.6 39.9 - - + -
118X LEU* 4.6 3.4 - - + -
119X ILE 3.3 7.9 - - - +
120X HIS* 3.7 21.5 - + + -
132X ASP* 4.4 3.4 - - + -
133X LEU* 1.3 76.6 - - - +
135X ALA* 1.3 60.7 + - - +
156X ALA* 5.6 1.5 + - + -
158X LEU* 3.7 29.6 - - + +
163X PHE* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25X VAL* 4.1 15.5 - - + -
27X ASP 3.4 9.2 - - - +
28X TYR* 4.7 2.5 - - + -
117X ALA 3.8 0.5 - - - +
118X LEU* 3.4 5.4 - - - +
119X ILE* 2.9 51.7 + - + +
133X LEU* 4.2 2.2 + - + -
134X TYR* 1.3 76.7 - - - +
136X VAL* 1.3 62.9 + - - +
137X LEU* 3.9 16.3 + - + +
163X PHE* 4.7 0.2 - - - -
185X FDD 4.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25X VAL* 3.5 5.4 - - - -
26X THR* 2.9 43.6 + - - +
27X ASP* 2.9 19.6 + - + +
117X ALA 3.4 5.4 - - - +
118X LEU* 4.1 11.0 - - + -
135X ALA* 1.3 73.4 - - - +
137X LEU* 1.3 66.1 + - - +
138X ASN* 6.1 0.4 - - + -
145X ALA* 4.4 7.2 - - + -
149X VAL* 4.1 26.7 - - + -
153X VAL* 4.1 10.3 - - + -
160X PHE* 4.1 16.2 - - + -
163X PHE* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17X TYR* 3.4 26.0 - - - +
23X TRP* 3.6 31.9 - - + -
24X TYR 3.1 7.2 - - - +
25X VAL* 3.6 31.6 - - + +
26X THR* 4.8 0.9 - - - -
44X LEU* 4.6 10.1 - - + -
116X SER* 3.3 6.4 - - - -
117X ALA* 2.8 38.5 + - + +
119X ILE* 3.9 18.8 - - + -
135X ALA* 4.1 15.5 - - + +
136X VAL* 1.3 84.3 - - - +
138X ASN* 1.3 62.9 + - - +
185X FDD 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23X TRP* 3.7 6.7 - - - -
24X TYR* 2.9 34.6 + - - +
26X THR* 4.1 13.4 - - + +
115X SER* 3.1 24.2 + - - +
116X SER* 4.0 13.5 - - - -
136X VAL* 6.1 0.4 - - + +
137X LEU* 1.3 73.6 + - - +
139X ARG* 1.3 64.8 + - - +
140X ASN* 2.8 35.9 + - - +
143X ALA* 3.4 27.9 + - + +
144X ALA 4.9 4.4 + - - -
145X ALA* 5.8 2.4 - - - +
149X VAL* 6.3 0.2 - - - +
----------------------------------------------------------
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