Contacts of the strand formed by residues 133 - 141 (chain B) in PDB entry 5IXC
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 133 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 3.0 9.2 - - - +
32B ARG* 2.7 79.5 + - + +
33B ASN* 5.3 3.4 - - - +
34B LEU* 5.0 0.9 - - - +
92B ILE* 5.1 0.2 - - - +
105B PHE* 4.4 3.4 - - - -
123B THR* 3.7 12.6 - - + +
124B PHE 3.2 5.2 - - - +
125B SER* 4.0 18.7 - - - -
131B GLU 3.9 9.9 - - - +
132B GLU* 1.3 82.1 - - - +
134B LEU* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 4.4 8.3 - - + -
30B GLU 3.4 17.7 - - - +
31B ALA* 4.0 6.1 - - + -
47B VAL* 4.3 12.6 - - + -
72B TRP* 4.1 11.0 - - + -
90B LEU* 3.3 37.0 - - + +
92B ILE* 4.0 23.3 - - + -
105B PHE* 4.0 26.2 - - + -
122B LYS 3.7 0.5 - - - +
123B THR* 3.3 1.9 - - - -
124B PHE* 2.8 39.2 + - + +
133B GLU* 1.3 75.7 - - - +
135B ASP* 1.3 64.2 + - - +
136B VAL* 3.9 12.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 4.2 0.2 - - - -
29B LEU* 3.0 45.1 + - + +
30B GLU* 2.8 21.4 + - + +
32B ARG* 2.9 37.5 + - - +
121B ARG* 5.7 6.8 - - + -
122B LYS 3.3 3.4 - - - +
123B THR* 2.7 31.2 + - - +
134B LEU* 1.3 72.9 - - - +
136B VAL* 1.3 66.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 4.5 8.5 - - + -
27B ARG 3.4 17.0 - - - +
28B VAL* 4.6 9.0 - - + -
29B LEU* 4.4 2.9 - - - -
90B LEU* 4.3 14.6 - - + -
120B LEU 3.8 0.5 - - - +
121B ARG* 3.5 3.3 - - - +
122B LYS* 2.8 40.2 + - - +
124B PHE* 4.4 9.6 - - + -
134B LEU* 4.1 24.0 - - + -
135B ASP* 1.3 80.1 - - - +
137B GLU* 1.3 69.2 + - - +
138B PHE* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR 3.7 0.9 - - - +
26B VAL* 3.3 6.1 - - - -
27B ARG* 2.9 72.5 + - + +
29B LEU* 4.1 14.7 - - + +
119B LEU* 4.2 24.7 - - + +
120B LEU 3.5 6.3 - - - +
121B ARG* 2.5 46.6 + - + +
136B VAL* 1.3 76.8 - - - +
138B PHE* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.2 11.9 - - + -
25B THR 3.5 1.1 - - - -
26B VAL* 3.7 26.5 - - + -
88B LEU* 3.7 27.4 - - + -
90B LEU* 4.6 1.3 - - + -
109B TYR* 3.5 40.8 - + - -
111B ILE* 5.1 1.3 - - + -
114B VAL* 3.8 23.1 - - + +
118B LYS 3.9 2.3 - - - +
119B LEU* 3.5 8.0 - - - +
120B LEU* 2.9 46.2 + - + +
122B LYS* 4.2 21.5 - - + -
124B PHE* 4.3 6.7 - + - -
136B VAL* 3.6 22.2 - - + -
137B GLU* 1.3 73.2 - - - +
139B LEU* 1.3 61.6 + - - +
140B MET 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN 3.3 5.0 - - - +
24B LEU* 4.2 1.7 - - - +
25B THR* 2.9 52.5 + - + +
114B VAL* 4.7 0.2 - - - -
117B GLY* 3.6 26.7 - - - +
118B LYS 4.2 2.0 - - - -
119B LEU* 3.9 31.0 - - + +
138B PHE* 1.3 73.6 - - - +
140B MET* 1.3 63.4 + - - +
141B GLU* 3.8 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TRP* 3.4 41.5 - - + +
23B GLN 3.4 3.6 - - - -
24B LEU* 3.7 29.2 - - + -
80B ILE* 4.5 18.2 - - + -
82B SER* 5.6 4.7 - - - -
111B ILE* 5.3 2.5 - - + +
114B VAL* 3.6 39.9 - - + +
115B LEU 3.9 4.7 + - - +
116B PRO* 3.3 23.4 - - + +
117B GLY* 2.9 29.8 + - - -
118B LYS 4.9 0.2 + - - -
139B LEU* 1.3 72.6 - - - +
141B GLU* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TRP* 3.2 8.4 - - - -
23B GLN* 2.8 58.7 + - + +
25B THR* 4.0 10.0 - - - +
116B PRO* 5.3 0.2 - - - -
117B GLY* 5.1 1.6 - - - +
139B LEU* 3.8 30.2 - - + +
140B MET* 1.3 78.3 - - - +
142B GLU* 1.3 69.8 + - - +
----------------------------------------------------------
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