Contacts of the strand formed by residues 130 - 139 (chain A) in PDB entry 1I04
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 GLU 130 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 3.1 41.9 + - - +
125A ASN* 4.0 1.0 - - - +
126A GLU* 3.8 1.6 - - - +
127A LYS* 3.3 28.8 + - + +
128A ASP 3.8 3.8 + - - -
129A GLY* 1.3 75.9 - - - +
131A THR* 1.3 82.8 + - - +
132A PHE* 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP* 5.3 0.9 - - - +
124A ILE* 3.8 23.3 - - + -
125A ASN 3.3 12.1 - - - +
126A GLU* 3.7 16.6 - - + +
129A GLY 4.0 3.7 + - - -
130A GLU* 1.3 88.3 + - - +
132A PHE* 1.3 69.9 + - - +
133A GLN* 5.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 3.3 23.6 - - - -
45A ASP* 3.4 13.2 - - - +
46A LYS* 3.9 19.7 - - + -
49A LYS* 3.8 36.3 - - + -
56A PHE* 3.7 34.3 - + - -
123A LEU* 4.6 0.7 - - + -
124A ILE* 3.7 2.6 - - - -
125A ASN* 3.0 69.9 + - + +
130A GLU* 4.8 2.0 - - - +
131A THR* 1.3 79.0 - - - +
133A GLN* 1.3 65.3 + - - +
134A LEU* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 2.9 29.2 + - - -
45A ASP* 2.8 25.1 + - - +
122A HIS* 2.7 31.9 + - - +
123A LEU 3.4 7.2 - - - +
124A ILE* 4.8 10.1 - - + -
131A THR* 5.7 2.9 - - + -
132A PHE* 1.3 77.7 - - - +
134A LEU* 1.3 61.7 + - - +
159A HIS* 2.9 40.6 + - - +
161A ILE* 4.5 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.6 8.5 - - + -
43A ALA 3.3 10.5 - - - +
44A SER* 4.7 0.4 - - - -
50A ILE* 3.9 16.4 - - + -
56A PHE* 3.6 43.1 - - + +
121A ALA* 4.9 3.1 - - + +
122A HIS* 3.5 5.2 - - - -
123A LEU* 2.7 58.2 + - + +
132A PHE* 3.9 12.3 - - + -
133A GLN* 1.3 77.3 - - - +
135A MET* 1.3 80.2 + - - +
136A GLY* 3.8 6.7 - - - +
138A TYR* 4.8 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.6 2.3 - - - -
43A ALA 2.7 31.0 + - - +
111A PRO* 4.6 2.9 - - + -
120A MET* 4.7 2.0 - - + -
121A ALA 3.3 13.0 - - - +
122A HIS* 3.5 36.8 - - + -
134A LEU* 1.3 79.6 - - - +
136A GLY* 1.3 57.9 + - - +
152A PHE* 3.5 33.3 - - + -
155A LEU* 3.6 34.1 - - + -
156A CYS* 3.7 17.9 - - - -
159A HIS* 3.9 11.4 - - - +
161A ILE* 3.5 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE 3.6 5.8 - - - -
42A LEU* 4.0 3.1 - - - -
119A LEU 3.6 0.9 - - - +
120A MET* 3.2 6.1 - - - -
121A ALA* 2.8 40.3 + - - -
134A LEU* 3.8 2.9 - - - +
135A MET* 1.3 75.2 - - - +
137A LEU* 1.3 59.7 + - - -
138A TYR* 3.6 26.3 - - - -
152A PHE* 3.4 5.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR 3.8 0.2 - - - -
40A ILE* 2.7 33.1 + - + +
41A ILE* 2.8 47.0 + - + +
118A PHE* 4.4 4.7 - - + -
119A LEU 3.5 3.1 - - - +
120A MET* 3.7 26.9 - - + -
136A GLY* 1.3 72.3 - - - -
138A TYR* 1.3 59.3 + - - +
144A LEU* 3.5 30.7 - - + -
148A ILE* 4.1 12.3 - - + -
149A LYS* 4.0 22.0 - - + -
152A PHE* 3.6 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TRP* 3.7 15.7 - - + -
38A HIS 3.0 16.8 - - - +
39A THR* 3.4 31.9 - - + -
40A ILE* 3.8 3.4 - - - -
42A LEU* 3.7 15.7 - - + +
58A LEU 4.8 2.0 + - - -
60A LEU* 3.7 33.2 - - + -
74A PHE* 5.2 6.6 - + - -
118A PHE* 3.2 5.0 - - - -
119A LEU* 2.8 58.0 + - + +
121A ALA* 4.0 15.9 - - + +
134A LEU* 4.8 5.9 - - - +
136A GLY* 3.6 26.0 - - - -
137A LEU* 1.3 73.7 - - - +
139A GLY* 1.3 58.2 + - - +
144A LEU* 3.8 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TRP* 3.5 6.2 - - - -
38A HIS* 2.9 32.0 + - - -
40A ILE* 3.4 9.6 - - - +
117A ASN 3.1 8.7 - - - -
138A TYR* 1.3 74.6 - - - +
140A ARG* 1.3 65.7 + - - -
141A GLU 3.0 16.1 + - - +
144A LEU* 4.1 7.9 - - - -
----------------------------------------------------------
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