Contacts of the strand formed by residues 117 - 122 (chain B) in PDB entry 1OQE
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 117 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 3.0 39.9 + - - +
43B LYS* 3.1 39.3 + - + -
44B ILE 3.2 8.7 - - - +
45B LEU* 3.9 10.7 - - + +
72B GLN 3.7 0.2 - - - +
73B ARG* 3.5 5.5 - - - +
74B LYS* 2.8 56.3 + - + +
115B GLY 3.8 9.4 - - - +
116B ASP* 1.3 79.2 - - - +
118B LEU* 1.3 63.6 + - - +
119B GLN* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 5.5 0.2 - - + -
43B LYS* 3.4 7.1 - - - +
44B ILE* 2.8 50.6 + - + +
46B VAL* 4.9 4.5 - - + -
54B ILE* 3.8 37.0 - - + -
71B ILE* 5.1 1.1 - - + -
72B GLN 3.2 12.1 - - - +
73B ARG* 4.2 7.6 - - + -
88B LEU* 4.2 4.3 - - + -
112B LEU* 3.8 36.8 - - + -
116B ASP* 6.1 0.2 - - + -
117B GLU* 1.3 78.6 - - - +
119B GLN* 1.3 61.6 - - - +
138B PHE* 4.0 12.3 - - + -
140B ALA* 4.2 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 4.1 27.2 - - + -
42B ASN 5.4 2.2 - - - +
43B LYS* 3.6 23.4 - - + +
70B LEU 3.5 0.9 - - - +
71B ILE* 3.5 3.6 - - - -
72B GLN* 2.8 67.4 + - + +
74B LYS* 3.5 32.6 - - + +
85B LEU* 4.1 9.9 - - - +
118B LEU* 1.3 77.5 - - - +
120B LEU* 1.3 61.5 + - - +
138B PHE* 3.7 10.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B THR 4.6 0.2 - - - +
24B PHE* 3.6 20.9 - - - -
25B VAL* 4.6 7.7 + - + -
27B TRP* 3.8 34.4 + - + +
42B ASN 5.9 0.2 + - - -
56B GLY* 4.4 8.5 - - - -
57B GLN 5.0 0.7 - - - +
58B VAL* 4.1 14.4 - - + -
69B HIS* 3.4 48.0 - - + +
70B LEU 3.3 4.5 - - - +
71B ILE* 4.0 16.8 - - + +
119B GLN* 1.3 72.4 - - - +
121B ALA* 1.3 66.0 + - - +
122B ILE* 4.4 5.2 - - + -
137B PHE 5.0 0.4 - - - +
138B PHE* 3.8 22.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 4.0 17.3 - - + -
23B THR 4.1 2.5 - - - -
24B PHE* 3.6 22.7 - - + -
69B HIS* 3.1 3.9 - - - -
70B LEU* 2.7 43.5 + - + +
72B GLN* 3.9 22.4 - - + +
119B GLN* 4.0 1.5 - - + +
120B LEU* 1.3 75.2 - - - +
122B ILE* 1.3 64.5 + - - +
123B PRO* 3.7 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 3.3 4.7 - - - -
23B THR* 2.7 50.8 + - + +
25B VAL* 4.2 20.9 - - + -
58B VAL* 4.3 4.7 - - + -
60B TYR* 4.1 10.8 - - + +
67B MET* 4.4 0.7 - - + -
68B GLY 3.4 14.4 - - - +
69B HIS* 4.0 13.2 - - + -
120B LEU* 4.4 4.0 - - + -
121B ALA* 1.3 78.2 - - - +
123B PRO* 1.3 54.9 - - + +
124B ARG* 2.8 23.1 + - + -
127B ALA* 3.8 23.1 - - + -
129B ILE* 3.9 29.8 - - + -
----------------------------------------------------------
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